diff --git a/services/clsi/app/coffee/ResourceWriter.coffee b/services/clsi/app/coffee/ResourceWriter.coffee
index 18b8122e1e..d0d19882d1 100644
--- a/services/clsi/app/coffee/ResourceWriter.coffee
+++ b/services/clsi/app/coffee/ResourceWriter.coffee
@@ -19,9 +19,14 @@ module.exports = ResourceWriter =
 			ResourceWriter.checkSyncState request.syncState, basePath, (error, syncStateOk) ->
 				logger.log syncState: request.syncState, result:syncStateOk, "checked state on incremental request"
 				return callback new Errors.FilesOutOfSyncError("invalid state for incremental update") if not syncStateOk
-				ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+				ResourceListManager.loadResourceList basePath, (error, resourceList) ->
 					return callback(error) if error?
-					ResourceListManager.loadResourceList basePath, callback
+					ResourceWriter._removeExtraneousFiles resourceList, basePath, (error) =>
+						return callback(error) if error?
+						ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+							return callback(error) if error?
+							callback(null, resourceList)
+
 		else
 			@saveAllResourcesToDisk request.project_id, request.resources, basePath, (error) ->
 				return callback(error) if error?
@@ -113,6 +118,8 @@ module.exports = ResourceWriter =
 					should_delete = true
 					if path.match(/^output\./) or path.match(/\.aux$/) or path.match(/^cache\//) # knitr cache
 						should_delete = false
+					if path in ['.project-resource-list', '.project-sync-state']
+						should_delete = false
 					if path == "output.pdf" or path == "output.dvi" or path == "output.log" or path == "output.xdv"
 						should_delete = true
 					if path == "output.tex" # created by TikzManager if present in output files
diff --git a/services/clsi/test/unit/coffee/ResourceWriterTests.coffee b/services/clsi/test/unit/coffee/ResourceWriterTests.coffee
index 0e602502f1..32ffb13227 100644
--- a/services/clsi/test/unit/coffee/ResourceWriterTests.coffee
+++ b/services/clsi/test/unit/coffee/ResourceWriterTests.coffee
@@ -23,7 +23,7 @@ describe "ResourceWriter", ->
 		@basePath = "/path/to/write/files/to"
 		@callback = sinon.stub()
 
-	describe "syncResourcesToDisk", ->
+	describe "syncResourcesToDisk on a full request", ->
 		beforeEach ->
 			@resources = [
 				"resource-1-mock"
@@ -36,7 +36,59 @@ describe "ResourceWriter", ->
 			@ResourceWriter.storeSyncState = sinon.stub().callsArg(2)
 			@ResourceListManager.saveResourceList = sinon.stub().callsArg(2)
 			@ResourceListManager.loadResourceList = sinon.stub().callsArg(1)
-			@ResourceWriter.syncResourcesToDisk({project_id: @project_id, resources: @resources}, @basePath, @callback)
+			@ResourceWriter.syncResourcesToDisk({
+				project_id: @project_id
+				syncState: @syncState = "0123456789abcdef"
+				resources: @resources
+			}, @basePath, @callback)
+
+		it "should remove old files", ->
+			@ResourceWriter._removeExtraneousFiles
+				.calledWith(@resources, @basePath)
+				.should.equal true
+
+		it "should write each resource to disk", ->
+			for resource in @resources
+				@ResourceWriter._writeResourceToDisk
+					.calledWith(@project_id, resource, @basePath)
+					.should.equal true
+
+		it "should store the sync state", ->
+			console.log "CHECKING", @syncState, @basePath
+			@ResourceWriter.storeSyncState
+				.calledWith(@syncState, @basePath)
+				.should.equal true
+
+		it "should save the resource list", ->
+			@ResourceListManager.saveResourceList
+				.calledWith(@resources, @basePath)
+				.should.equal true
+
+		it "should call the callback", ->
+			@callback.called.should.equal true
+
+	describe "syncResourcesToDisk on an incremental update", ->
+		beforeEach ->
+			@resources = [
+				"resource-1-mock"
+			]
+			@ResourceWriter._writeResourceToDisk = sinon.stub().callsArg(3)
+			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArg(2)
+			@ResourceWriter.checkSyncState = sinon.stub().callsArgWith(2, null, true)
+			@ResourceWriter.storeSyncState = sinon.stub().callsArg(2)
+			@ResourceListManager.saveResourceList = sinon.stub().callsArg(2)
+			@ResourceListManager.loadResourceList = sinon.stub().callsArg(1)
+			@ResourceWriter.syncResourcesToDisk({
+				project_id: @project_id,
+				syncType: "incremental",
+				syncState: @syncState = "1234567890abcdef",
+				resources: @resources
+			}, @basePath, @callback)
+
+		it "should check the sync state matches", ->
+			@ResourceWriter.checkSyncState
+				.calledWith(@syncState, @basePath)
+				.should.equal true
 
 		it "should remove old files", ->
 			@ResourceWriter._removeExtraneousFiles