diff --git a/app/coffee/OutputFileFinder.coffee b/app/coffee/OutputFileFinder.coffee
index c89cc8a..80bd07f 100644
--- a/app/coffee/OutputFileFinder.coffee
+++ b/app/coffee/OutputFileFinder.coffee
@@ -5,7 +5,7 @@ spawn = require("child_process").spawn
 logger = require "logger-sharelatex"
 
 module.exports = OutputFileFinder =
-	findOutputFiles: (resources, directory, callback = (error, outputFiles) ->) ->
+	findOutputFiles: (resources, directory, callback = (error, outputFiles, allFiles) ->) ->
 		incomingResources = {}
 		for resource in resources
 			incomingResources[resource.path] = true
@@ -16,7 +16,6 @@ module.exports = OutputFileFinder =
 			if error?
 				logger.err err:error, "error finding all output files"
 				return callback(error)
-			jobs = []
 			outputFiles = []
 			for file in allFiles
 				if !incomingResources[file]
@@ -24,7 +23,7 @@ module.exports = OutputFileFinder =
 						path: file
 						type: file.match(/\.([^\.]+)$/)?[1]
 					}
-			callback null, outputFiles
+			callback null, outputFiles, allFiles
 
 	_getAllFiles: (directory, _callback = (error, fileList) ->) ->
 		callback = (error, fileList) ->
diff --git a/app/coffee/ResourceStateManager.coffee b/app/coffee/ResourceStateManager.coffee
index 7f97405..247c929 100644
--- a/app/coffee/ResourceStateManager.coffee
+++ b/app/coffee/ResourceStateManager.coffee
@@ -49,3 +49,15 @@ module.exports = ResourceStateManager =
 			else
 				resources = ({path: path} for path in resourceList)
 				callback(null, resources)
+
+	checkResourceFiles: (resources, allFiles, directory, callback = (error) ->) ->
+		# check if any of the input files are not present in list of files
+		seenFile = {}
+		for file in allFiles
+			seenFile[file] = true
+		missingFiles = (resource.path for resource in resources when not seenFile[resource.path])
+		if missingFiles.length > 0
+			logger.err missingFiles:missingFiles, dir:directory, allFiles:allFiles, resources:resources, "missing input files for project"
+			return callback new Errors.FilesOutOfSyncError("resource files missing in incremental update")
+		else
+			callback()
diff --git a/app/coffee/ResourceWriter.coffee b/app/coffee/ResourceWriter.coffee
index 55f1508..fa5b010 100644
--- a/app/coffee/ResourceWriter.coffee
+++ b/app/coffee/ResourceWriter.coffee
@@ -18,11 +18,13 @@ module.exports = ResourceWriter =
 			logger.log project_id: request.project_id, user_id: request.user_id, "incremental sync"
 			ResourceStateManager.checkProjectStateHashMatches request.syncState, basePath, (error, resourceList) ->
 				return callback(error) if error?
-				ResourceWriter._removeExtraneousFiles resourceList, basePath, (error) =>
+				ResourceWriter._removeExtraneousFiles resourceList, basePath, (error, outputFiles, allFiles) ->
 					return callback(error) if error?
-					ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+					ResourceStateManager.checkResourceFiles resourceList, allFiles, basePath, (error) ->
 						return callback(error) if error?
-						callback(null, resourceList)
+						ResourceWriter.saveIncrementalResourcesToDisk request.project_id, request.resources, basePath, (error) ->
+							return callback(error) if error?
+							callback(null, resourceList)
 		else
 			logger.log project_id: request.project_id, user_id: request.user_id, "full sync"
 			@saveAllResourcesToDisk request.project_id, request.resources, basePath, (error) ->
@@ -60,13 +62,13 @@ module.exports = ResourceWriter =
 			else
 				return callback()
 
-	_removeExtraneousFiles: (resources, basePath, _callback = (error) ->) ->
+	_removeExtraneousFiles: (resources, basePath, _callback = (error, outputFiles, allFiles) ->) ->
 		timer = new Metrics.Timer("unlink-output-files")
-		callback = (error) ->
+		callback = (error, result...) ->
 			timer.done()
-			_callback(error)
+			_callback(error, result...)
 
-		OutputFileFinder.findOutputFiles resources, basePath, (error, outputFiles) ->
+		OutputFileFinder.findOutputFiles resources, basePath, (error, outputFiles, allFiles) ->
 			return callback(error) if error?
 
 			jobs = []
@@ -85,7 +87,9 @@ module.exports = ResourceWriter =
 					if should_delete
 						jobs.push (callback) -> ResourceWriter._deleteFileIfNotDirectory Path.join(basePath, path), callback
 
-			async.series jobs, callback
+			async.series jobs, (error) ->
+				return callback(error) if error?
+				callback(null, outputFiles, allFiles)
 
 	_deleteFileIfNotDirectory: (path, callback = (error) ->) ->
 		fs.stat path, (error, stat) ->
diff --git a/test/unit/coffee/ResourceWriterTests.coffee b/test/unit/coffee/ResourceWriterTests.coffee
index 520db6f..dee0952 100644
--- a/test/unit/coffee/ResourceWriterTests.coffee
+++ b/test/unit/coffee/ResourceWriterTests.coffee
@@ -32,7 +32,6 @@ describe "ResourceWriter", ->
 			]
 			@ResourceWriter._writeResourceToDisk = sinon.stub().callsArg(3)
 			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArg(2)
-			@ResourceStateManager.checkProjectStateHashMatches = sinon.stub().callsArg(2)
 			@ResourceStateManager.saveProjectStateHash = sinon.stub().callsArg(3)
 			@ResourceWriter.syncResourcesToDisk({
 				project_id: @project_id
@@ -65,9 +64,10 @@ describe "ResourceWriter", ->
 				"resource-1-mock"
 			]
 			@ResourceWriter._writeResourceToDisk = sinon.stub().callsArg(3)
-			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArg(2)
+			@ResourceWriter._removeExtraneousFiles = sinon.stub().callsArgWith(2, null, @outputFiles = [], @allFiles = [])
 			@ResourceStateManager.checkProjectStateHashMatches = sinon.stub().callsArgWith(2, null, @resources)
 			@ResourceStateManager.saveProjectStateHash = sinon.stub().callsArg(3)
+			@ResourceStateManager.checkResourceFiles = sinon.stub().callsArg(3)
 			@ResourceWriter.syncResourcesToDisk({
 				project_id: @project_id,
 				syncType: "incremental",
@@ -85,6 +85,11 @@ describe "ResourceWriter", ->
 				.calledWith(@resources, @basePath)
 				.should.equal true
 
+		it "should check each resource exists", ->
+			@ResourceStateManager.checkResourceFiles
+				.calledWith(@resources, @allFiles, @basePath)
+				.should.equal true
+
 		it "should write each resource to disk", ->
 			for resource in @resources
 				@ResourceWriter._writeResourceToDisk