If the in built quota management in Server 2008 R2 is misreporting the amount of space used in a folder you can use the tool dirquota that comes with the File Server Resource Manager, https://technet.microsoft.com/en-us/library/cc732431(v=ws.11).aspx.
It has many features but to clear the problem discussed you can rescan the folder using the following in an Administrator Command prompt
dirquota quota scan /path:path_to_folder
Then to view if the scan has been successful use
dirquota quota list /path:path_to_folder
This should show what the use is now and the management console should now show the correct size when refreshed.