Try this Fix It Tool first from Microsoft. I don’t know if this will fix it but it could.

https://support.microsoft.com/en-us/kb/3038627

Last time I deleted the cache files for SharePoint and resynced the libraries to fix syncing issues. This is going to remove the synced files from the computer. The user will no longer have access to the SharePoint libraries until you sync them again from the web interface. Please set the expectation that this will have to download all of the content again from the SharePoint site and the user may experience some slowness until that is done.

Follow these steps:

1. Stop Sync For All Folders.

a) Right click the “OneDrive for Business” Icon in you task bar.
b) Click “Stop Syncing a folder”, to let a popup window appear which lists all the document libraries.
c) “Stop syncing” all the libraries. After that, none of the document libraries will be listed in the popup window.

2. Backup all the local documents & files in your document libraries to another place. This may not be necessary but I just renamed the folders for the files with a .old at the end.
3. After the backup work is done, remove the original documents & files in your local OneDrive for Business folder.
4. Cache clearing for OneDrive for Business.

a) Right click on the Windows status bar, select Start Task Manager, and get a list of running processes by clicking the “Processes” tab.
b) Verify that none of the following processes are running, if they are running please right-click and End Process.

groove.exe
msosync.exe
msouc.exe
winword.exe
excel.exe
powerpnt.exe

5) Close all the application you are running in you system. (Word, Excel, Power Point, etc…)

6) Give yourself an administrator role as follows:

Click the start button and type cmd in the search bar. When cmd.exe appears in the results, right-click it and select Run as Administrator.

7) At the command prompt, delete the Office file cache and Spw folders by issuing four commands as follows:

Type “cd %USERPROFILE%\AppData\Local\Microsoft\Office\15.0\” and then press the Enter key.
Type “rmdir OfficeFileCache /s” and then press the Enter key.
Type “cd %USERPROFILE%\AppData\Local\Microsoft\Office\” and then press the Enter key.
Type “rmdir Spw /s” and then press the Enter key.

8) If you get an error when executing either rmdir command, one of the .exe processes is probably still running. Correct the problem by returning to the Task Manager (step 2), stopping the processes, and then removing the directories as described previously.

9) Reboot the Computer.

When above steps are done and with no errors, please go to your online libraries and sync them again.

After you sync the libraries again the issue should be resolved.