Having a problem renaming or deleting a file / folder that is referenced by SQL Server or SSIS? Here’s a tip.
If you’re trying to rename or delete a directory folder / file and keep getting a "File being used by another application" error, check to see if you have BIDS (Business Intelligence Development Studio) open. Even after closing the project / SSIS package that used the folder, BIDS may be hanging on to the folder connection which will prevent you from doing cleanup work on the directory. Close BIDS and all related files (config file, etc.) and you should be able rename or delete the folder / file in question.
I hope that helps someone.

