diff --git a/services/web/app/src/Features/Project/ProjectEntityHandler.js b/services/web/app/src/Features/Project/ProjectEntityHandler.js
index fb219382ee..0b8a2e3b1a 100644
--- a/services/web/app/src/Features/Project/ProjectEntityHandler.js
+++ b/services/web/app/src/Features/Project/ProjectEntityHandler.js
@@ -20,15 +20,11 @@ const ProjectEntityHandler = {
       }
 
       ProjectEntityHandler._getAllFolders(projectId, (error, folders) => {
-        if (folders == null) {
-          folders = {}
-        }
         if (error != null) {
           return callback(error)
         }
         const docs = {}
-        for (const folderPath in folders) {
-          const folder = folders[folderPath]
+        for (const { path: folderPath, folder } of folders) {
           for (const doc of folder.docs || []) {
             const content = docContents[doc._id.toString()]
             if (content != null) {
@@ -49,15 +45,11 @@ const ProjectEntityHandler = {
 
   getAllFiles(projectId, callback) {
     ProjectEntityHandler._getAllFolders(projectId, (err, folders) => {
-      if (folders == null) {
-        folders = {}
-      }
       if (err != null) {
         return callback(err)
       }
       const files = {}
-      for (const folderPath in folders) {
-        const folder = folders[folderPath]
+      for (const { path: folderPath, folder } of folders) {
         for (const file of folder.fileRefs || []) {
           if (file != null) {
             files[path.join(folderPath, file.name)] = file
@@ -83,16 +75,12 @@ const ProjectEntityHandler = {
 
   getAllEntitiesFromProject(project, callback) {
     ProjectEntityHandler._getAllFoldersFromProject(project, (err, folders) => {
-      if (folders == null) {
-        folders = {}
-      }
       if (err != null) {
         return callback(err)
       }
       const docs = []
       const files = []
-      for (const folderPath in folders) {
-        const folder = folders[folderPath]
+      for (const { path: folderPath, folder } of folders) {
         for (const doc of folder.docs || []) {
           if (doc != null) {
             docs.push({ path: path.join(folderPath, doc.name), doc })
@@ -122,15 +110,11 @@ const ProjectEntityHandler = {
 
   getAllDocPathsFromProject(project, callback) {
     ProjectEntityHandler._getAllFoldersFromProject(project, (err, folders) => {
-      if (folders == null) {
-        folders = {}
-      }
       if (err != null) {
         return callback(err)
       }
       const docPath = {}
-      for (const folderPath in folders) {
-        const folder = folders[folderPath]
+      for (const { path: folderPath, folder } of folders) {
         for (const doc of folder.docs || []) {
           docPath[doc._id] = path.join(folderPath, doc.name)
         }
@@ -226,9 +210,9 @@ const ProjectEntityHandler = {
   },
 
   _getAllFoldersFromProject(project, callback) {
-    const folders = {}
+    const folders = []
     function processFolder(basePath, folder) {
-      folders[basePath] = folder
+      folders.push({ path: basePath, folder })
       for (const childFolder of folder.folders || []) {
         if (childFolder.name != null) {
           processFolder(path.join(basePath, childFolder.name), childFolder)
diff --git a/services/web/app/src/Features/Project/ProjectEntityUpdateHandler.js b/services/web/app/src/Features/Project/ProjectEntityUpdateHandler.js
index 369f2ca492..50e97b6a2d 100644
--- a/services/web/app/src/Features/Project/ProjectEntityUpdateHandler.js
+++ b/services/web/app/src/Features/Project/ProjectEntityUpdateHandler.js
@@ -1355,25 +1355,34 @@ const ProjectEntityUpdateHandler = {
             if (error != null) {
               return callback(error)
             }
-
-            docs = _.map(docs, doc => ({
-              doc: doc.doc._id,
-              path: doc.path,
-            }))
-
-            files = _.map(files, file => ({
-              file: file.file._id,
-              path: file.path,
-              url: FileStoreHandler._buildUrl(projectId, file.file._id),
-              _hash: file.file.hash,
-            }))
-
-            DocumentUpdaterHandler.resyncProjectHistory(
+            ProjectEntityUpdateHandler._checkFiletree(
               projectId,
               projectHistoryId,
-              docs,
-              files,
-              callback
+              [...docs, ...files],
+              error => {
+                if (error) {
+                  return callback(error)
+                }
+                docs = _.map(docs, doc => ({
+                  doc: doc.doc._id,
+                  path: doc.path,
+                }))
+
+                files = _.map(files, file => ({
+                  file: file.file._id,
+                  path: file.path,
+                  url: FileStoreHandler._buildUrl(projectId, file.file._id),
+                  _hash: file.file.hash,
+                }))
+
+                DocumentUpdaterHandler.resyncProjectHistory(
+                  projectId,
+                  projectHistoryId,
+                  docs,
+                  files,
+                  callback
+                )
+              }
             )
           }
         )
@@ -1381,6 +1390,91 @@ const ProjectEntityUpdateHandler = {
     )
   ),
 
+  _checkFiletree(projectId, projectHistoryId, entities, callback) {
+    const renames = []
+    const paths = new Map()
+    for (const entity of entities) {
+      // if the path is invalid (i.e. not going to be accepted in
+      // project-history due to filename rules) we could also flag it for a
+      // rename here.
+      if (paths.has(entity.path)) {
+        renames.push(entity)
+      } else {
+        paths.set(entity.path, entity)
+      }
+    }
+    if (renames.length === 0) {
+      return callback()
+    }
+    logger.warn({ projectId, renames }, 'found conflict in filetree')
+    // find new names for duplicate files
+    for (const entity of renames) {
+      const {
+        newPath,
+        newName,
+      } = ProjectEntityUpdateHandler.findNextAvailableName(paths, entity)
+      logger.debug({ projectId, newName, newPath }, 'found new name')
+      entity.newPath = newPath
+      entity.newName = newName
+    }
+    // rename the duplicate files
+    const doRename = (entity, cb) => {
+      const entityId = entity.doc ? entity.doc._id : entity.file._id
+      const entityType = entity.doc ? 'doc' : 'file'
+      ProjectEntityMongoUpdateHandler.renameEntity(
+        projectId,
+        entityId,
+        entityType,
+        entity.newName,
+        (err, project, startPath, endPath, rev, changes) => {
+          if (err) {
+            return cb(err)
+          }
+          // update the renamed entity for the resync
+          entity.path = entity.newPath
+          if (entityType === 'doc') {
+            entity.doc.name = entity.newName
+          } else {
+            entity.file.name = entity.newName
+          }
+          delete entity.newPath
+          delete entity.newname
+          DocumentUpdaterHandler.updateProjectStructure(
+            projectId,
+            projectHistoryId,
+            null,
+            changes,
+            cb
+          )
+        }
+      )
+    }
+    async.eachSeries(renames, doRename, callback)
+  },
+
+  findNextAvailableName(allPaths, entity) {
+    const incrementReplacer = (match, p1) => {
+      return ' (' + (parseInt(p1, 10) + 1) + ')'
+    }
+    let candidatePath = entity.path
+    // if the filename was invalid we should normalise it here too.  Currently
+    // this only handles renames in the same folder, so we will be out of luck
+    // if it is the folder name which in invalid.  We could handle folder
+    // renames by returning the folders list from getAllEntitiesFromProject
+    do {
+      // does the filename look like "foo (1)" if so, increment the number in parentheses
+      if (/ \(\d+\)$/.test(candidatePath)) {
+        candidatePath = candidatePath.replace(/ \((\d+)\)$/, incrementReplacer)
+      } else {
+        // otherwise, add a ' (1)' suffix to the name
+        candidatePath = candidatePath + ' (1)'
+      }
+    } while (allPaths.has(candidatePath)) // keep going until the name is unique
+    // add the new name to the set
+    allPaths.set(candidatePath, entity)
+    return { newPath: candidatePath, newName: candidatePath.split('/').pop() }
+  },
+
   isPathValidForRootDoc(docPath) {
     const docExtension = Path.extname(docPath)
     return VALID_ROOT_DOC_REGEXP.test(docExtension)
diff --git a/services/web/test/unit/src/Project/ProjectEntityHandlerTests.js b/services/web/test/unit/src/Project/ProjectEntityHandlerTests.js
index ecc4ff48bc..186a76f838 100644
--- a/services/web/test/unit/src/Project/ProjectEntityHandlerTests.js
+++ b/services/web/test/unit/src/Project/ProjectEntityHandlerTests.js
@@ -1,53 +1,26 @@
-/* eslint-disable
-    camelcase,
-    max-len,
-    no-return-assign,
-    no-unused-vars,
-*/
-// TODO: This file was created by bulk-decaffeinate.
-// Fix any style issues and re-enable lint.
-/*
- * decaffeinate suggestions:
- * DS102: Remove unnecessary code created because of implicit returns
- * DS205: Consider reworking code to avoid use of IIFEs
- * DS206: Consider reworking classes to avoid initClass
- * Full docs: https://github.com/decaffeinate/decaffeinate/blob/master/docs/suggestions.md
- */
-const { assert, expect } = require('chai')
+const { expect } = require('chai')
 const sinon = require('sinon')
 const modulePath = '../../../../app/src/Features/Project/ProjectEntityHandler'
 const SandboxedModule = require('sandboxed-module')
 const Errors = require('../../../../app/src/Features/Errors/Errors')
 
 describe('ProjectEntityHandler', function () {
-  const project_id = '4eecb1c1bffa66588e0000a1'
-  const doc_id = '4eecb1c1bffa66588e0000a2'
-  const folder_id = '4eecaffcbffa66588e000008'
-  const rootFolderId = '4eecaffcbffa66588e000007'
-  const userId = 1234
+  const projectId = '4eecb1c1bffa66588e0000a1'
+  const docId = '4eecb1c1bffa66588e0000a2'
 
   beforeEach(function () {
-    let Project
     this.TpdsUpdateSender = {
       addDoc: sinon.stub().callsArg(1),
       addFile: sinon.stub().callsArg(1),
     }
-    this.ProjectModel = Project = (function () {
-      Project = class Project {
-        static initClass() {
-          this.prototype.rootFolder = [this.rootFolder]
-        }
-
-        constructor(options) {
-          this._id = project_id
-          this.name = 'project_name_here'
-          this.rev = 0
-        }
+    this.ProjectModel = class Project {
+      constructor(options) {
+        this._id = projectId
+        this.name = 'project_name_here'
+        this.rev = 0
+        this.rootFolder = [this.rootFolder]
       }
-      Project.initClass()
-      return Project
-    })()
-
+    }
     this.project = new this.ProjectModel()
 
     this.ProjectLocator = { findElement: sinon.stub() }
@@ -56,7 +29,7 @@ describe('ProjectEntityHandler', function () {
     }
     this.callback = sinon.stub()
 
-    return (this.ProjectEntityHandler = SandboxedModule.require(modulePath, {
+    this.ProjectEntityHandler = SandboxedModule.require(modulePath, {
       requires: {
         '../Docstore/DocstoreManager': (this.DocstoreManager = {}),
         '../../Features/DocumentUpdater/DocumentUpdaterHandler': this
@@ -68,7 +41,7 @@ describe('ProjectEntityHandler', function () {
         './ProjectGetter': (this.ProjectGetter = {}),
         '../ThirdPartyDataStore/TpdsUpdateSender': this.TpdsUpdateSender,
       },
-    }))
+    })
   })
 
   describe('getting folders, docs and files', function () {
@@ -131,13 +104,11 @@ describe('ProjectEntityHandler', function () {
         this.DocstoreManager.getAllDocs = sinon
           .stub()
           .callsArgWith(1, null, this.docs)
-        this.ProjectEntityHandler.getAllDocs(project_id, this.callback)
+        this.ProjectEntityHandler.getAllDocs(projectId, this.callback)
       })
 
       it('should get the doc lines and rev from the docstore', function () {
-        this.DocstoreManager.getAllDocs
-          .calledWith(project_id)
-          .should.equal(true)
+        this.DocstoreManager.getAllDocs.calledWith(projectId).should.equal(true)
       })
 
       it('should call the callback with the docs with the lines and rev included', function () {
@@ -163,7 +134,7 @@ describe('ProjectEntityHandler', function () {
     describe('getAllFiles', function () {
       beforeEach(function () {
         this.callback = sinon.stub()
-        this.ProjectEntityHandler.getAllFiles(project_id, this.callback)
+        this.ProjectEntityHandler.getAllFiles(projectId, this.callback)
       })
 
       it('should call the callback with the files', function () {
@@ -197,7 +168,7 @@ describe('ProjectEntityHandler', function () {
         )
       })
 
-      it('should call the callback with the path for each doc_id', function () {
+      it('should call the callback with the path for each docId', function () {
         this.expected = {}
         this.expected[this.doc1._id] = `/${this.doc1.name}`
         this.expected[this.doc2._id] = `/folder1/${this.doc2.name}`
@@ -211,7 +182,7 @@ describe('ProjectEntityHandler', function () {
       })
       it('should call the callback with the path for an existing doc id at the root level', function () {
         this.ProjectEntityHandler.getDocPathByProjectIdAndDocId(
-          project_id,
+          projectId,
           this.doc1._id,
           this.callback
         )
@@ -220,7 +191,7 @@ describe('ProjectEntityHandler', function () {
 
       it('should call the callback with the path for an existing doc id nested within a folder', function () {
         this.ProjectEntityHandler.getDocPathByProjectIdAndDocId(
-          project_id,
+          projectId,
           this.doc2._id,
           this.callback
         )
@@ -231,7 +202,7 @@ describe('ProjectEntityHandler', function () {
 
       it('should call the callback with a NotFoundError for a non-existing doc', function () {
         this.ProjectEntityHandler.getDocPathByProjectIdAndDocId(
-          project_id,
+          projectId,
           'non-existing-id',
           this.callback
         )
@@ -242,7 +213,7 @@ describe('ProjectEntityHandler', function () {
 
       it('should call the callback with a NotFoundError for an existing file', function () {
         this.ProjectEntityHandler.getDocPathByProjectIdAndDocId(
-          project_id,
+          projectId,
           this.file1._id,
           this.callback
         )
@@ -255,21 +226,21 @@ describe('ProjectEntityHandler', function () {
     describe('_getAllFolders', function () {
       beforeEach(function () {
         this.callback = sinon.stub()
-        this.ProjectEntityHandler._getAllFolders(project_id, this.callback)
+        this.ProjectEntityHandler._getAllFolders(projectId, this.callback)
       })
 
       it('should get the project without the docs lines', function () {
         this.ProjectGetter.getProjectWithoutDocLines
-          .calledWith(project_id)
+          .calledWith(projectId)
           .should.equal(true)
       })
 
       it('should call the callback with the folders', function () {
         this.callback
-          .calledWith(null, {
-            '/': this.project.rootFolder[0],
-            '/folder1': this.folder1,
-          })
+          .calledWith(null, [
+            { path: '/', folder: this.project.rootFolder[0] },
+            { path: '/folder1', folder: this.folder1 },
+          ])
           .should.equal(true)
       })
     })
@@ -285,10 +256,10 @@ describe('ProjectEntityHandler', function () {
 
       it('should call the callback with the folders', function () {
         this.callback
-          .calledWith(null, {
-            '/': this.project.rootFolder[0],
-            '/folder1': this.folder1,
-          })
+          .calledWith(null, [
+            { path: '/', folder: this.project.rootFolder[0] },
+            { path: '/folder1', folder: this.folder1 },
+          ])
           .should.equal(true)
       })
     })
@@ -304,12 +275,12 @@ describe('ProjectEntityHandler', function () {
       this.DocstoreManager.getDoc = sinon
         .stub()
         .callsArgWith(3, null, this.lines, this.rev, this.version, this.ranges)
-      this.ProjectEntityHandler.getDoc(project_id, doc_id, this.callback)
+      this.ProjectEntityHandler.getDoc(projectId, docId, this.callback)
     })
 
     it('should call the docstore', function () {
       this.DocstoreManager.getDoc
-        .calledWith(project_id, doc_id)
+        .calledWith(projectId, docId)
         .should.equal(true)
     })
 
@@ -332,15 +303,12 @@ describe('ProjectEntityHandler', function () {
       this.DocstoreManager.getDoc = sinon
         .stub()
         .callsArgWith(3, null, this.lines, this.rev, this.version, this.ranges)
-      result = await this.ProjectEntityHandler.promises.getDoc(
-        project_id,
-        doc_id
-      )
+      result = await this.ProjectEntityHandler.promises.getDoc(projectId, docId)
     })
 
     it('should call the docstore', function () {
       this.DocstoreManager.getDoc
-        .calledWith(project_id, doc_id)
+        .calledWith(projectId, docId)
         .should.equal(true)
     })
 
diff --git a/services/web/test/unit/src/Project/ProjectEntityUpdateHandlerTests.js b/services/web/test/unit/src/Project/ProjectEntityUpdateHandlerTests.js
index 01e602d553..2a29b280d0 100644
--- a/services/web/test/unit/src/Project/ProjectEntityUpdateHandlerTests.js
+++ b/services/web/test/unit/src/Project/ProjectEntityUpdateHandlerTests.js
@@ -78,7 +78,7 @@ describe('ProjectEntityUpdateHandler', function () {
       flushDocToMongo: sinon.stub().yields(),
       updateProjectStructure: sinon.stub().yields(),
       setDocument: sinon.stub(),
-      resyncProjectHistory: sinon.stub(),
+      resyncProjectHistory: sinon.stub().yields(),
       deleteDoc: sinon.stub().yields(),
     }
     this.fs = {
@@ -118,7 +118,7 @@ describe('ProjectEntityUpdateHandler', function () {
       replaceFileWithNew: sinon.stub(),
       mkdirp: sinon.stub(),
       moveEntity: sinon.stub(),
-      renameEntity: sinon.stub(),
+      renameEntity: sinon.stub().yields(),
       deleteEntity: sinon.stub(),
       replaceDocWithFile: sinon.stub(),
       replaceFileWithDoc: sinon.stub(),
@@ -136,6 +136,11 @@ describe('ProjectEntityUpdateHandler', function () {
       copyFile: sinon.stub(),
       uploadFileFromDisk: sinon.stub(),
       deleteFile: sinon.stub(),
+      _buildUrl: sinon
+        .stub()
+        .callsFake(
+          (projectId, fileId) => `www.filestore.test/${projectId}/${fileId}`
+        ),
     }
     this.FileWriter = {
       writeLinesToDisk: sinon.stub(),
@@ -1940,10 +1945,6 @@ describe('ProjectEntityUpdateHandler', function () {
           docs,
           files
         )
-        this.FileStoreHandler._buildUrl = (projectId, fileId) =>
-          `www.filestore.test/${projectId}/${fileId}`
-        this.DocumentUpdaterHandler.resyncProjectHistory.yields()
-
         this.ProjectEntityUpdateHandler.resyncProjectHistory(
           projectId,
           this.callback
@@ -1984,6 +1985,100 @@ describe('ProjectEntityUpdateHandler', function () {
         this.callback.called.should.equal(true)
       })
     })
+
+    describe('a project with duplicate filenames', function () {
+      beforeEach(function (done) {
+        this.ProjectGetter.getProject.yields(null, this.project)
+        this.docs = [
+          { doc: { _id: 'doc1' }, path: 'main.tex' },
+          { doc: { _id: 'doc2' }, path: 'a/b/c/duplicate.tex' },
+          { doc: { _id: 'doc3' }, path: 'a/b/c/duplicate.tex' },
+          { doc: { _id: 'doc4' }, path: 'another dupe (22)' },
+          { doc: { _id: 'doc5' }, path: 'a/b/c/duplicate.tex' },
+        ]
+        this.files = [
+          { file: { _id: 'file1', hash: 'hash1' }, path: 'image.jpg' },
+          { file: { _id: 'file2', hash: 'hash2' }, path: 'duplicate.jpg' },
+          { file: { _id: 'file3', hash: 'hash3' }, path: 'duplicate.jpg' },
+          { file: { _id: 'file4', hash: 'hash4' }, path: 'another dupe (22)' },
+        ]
+        this.ProjectEntityHandler.getAllEntitiesFromProject.yields(
+          null,
+          this.docs,
+          this.files
+        )
+        this.ProjectEntityUpdateHandler.resyncProjectHistory(projectId, done)
+      })
+
+      it('renames the duplicate files', function () {
+        const renameEntity = this.ProjectEntityMongoUpdateHandler.renameEntity
+        expect(renameEntity).to.have.callCount(4)
+        expect(renameEntity).to.have.been.calledWith(
+          projectId,
+          'doc3',
+          'doc',
+          'duplicate.tex (1)'
+        )
+        expect(renameEntity).to.have.been.calledWith(
+          projectId,
+          'doc5',
+          'doc',
+          'duplicate.tex (2)'
+        )
+        expect(renameEntity).to.have.been.calledWith(
+          projectId,
+          'file3',
+          'file',
+          'duplicate.jpg (1)'
+        )
+        expect(renameEntity).to.have.been.calledWith(
+          projectId,
+          'file4',
+          'file',
+          'another dupe (23)'
+        )
+      })
+
+      it('tells the doc updater to resync the project', function () {
+        const docs = [
+          { doc: 'doc1', path: 'main.tex' },
+          { doc: 'doc2', path: 'a/b/c/duplicate.tex' },
+          { doc: 'doc3', path: 'a/b/c/duplicate.tex (1)' },
+          { doc: 'doc4', path: 'another dupe (22)' },
+          { doc: 'doc5', path: 'a/b/c/duplicate.tex (2)' },
+        ]
+        const urlPrefix = `www.filestore.test/${projectId}`
+        const files = [
+          {
+            file: 'file1',
+            path: 'image.jpg',
+            url: `${urlPrefix}/file1`,
+            _hash: 'hash1',
+          },
+          {
+            file: 'file2',
+            path: 'duplicate.jpg',
+            url: `${urlPrefix}/file2`,
+            _hash: 'hash2',
+          },
+          {
+            file: 'file3',
+            path: 'duplicate.jpg (1)',
+            url: `${urlPrefix}/file3`,
+            _hash: 'hash3',
+          },
+          {
+            file: 'file4',
+            path: 'another dupe (23)',
+            url: `${urlPrefix}/file4`,
+            _hash: 'hash4',
+          },
+        ]
+        expect(
+          this.DocumentUpdaterHandler.resyncProjectHistory
+        ).to.have.been.calledWith(projectId, projectHistoryId, docs, files)
+      })
+    })
   })
 
   describe('_cleanUpEntity', function () {