I just run in to some sync issues with Skydrive Pro, this is what is solved my problem. All steps I found them are from this blog: http://guru365.net/2013/06/25/skydrive-pro-synchronisation-issues-skydrive/
Below are the steps I have ran through to resolve synchronization issues;
To begin try the first 4 steps to see if this resolves your issue.
1. In SkyDrive Pro select “Stop Syncing a Folder”
2. Delete the SkyDrive folder on the local machine
3. Clear all browsing history in IE
4. Use Disk Clean up to remove temporary files
If you are still experiencing issues please try the following, I would recommend an administrator complete these tasks if you are experiencing this as a regular user.
1. Ensure that any Office processes are not running, groove.exe (SkyDrive Pro), msouc.exe, msosync.exe, office library sync,…
2. Open Windows explorer and browse toC:\Users\%username%\AppData\Local\Microsoft\Office\SpwC:\Users\%username%\AppData\Local\Microsoft\Office\15.0\OfficeFileCach
Delete all the contents.
3. This is an extra step which was not mentioned on that blog: If you don’t want to end up with duplicate libraries in your sync folder on your computer, you need to go and delete old library (the one that say Skydrive @ yourdomain) and the folders inside. Don’t worry they will get synched back from Skydrive’s portal.
4. Reconfigure a document library which you want to sync.