Not a direct solution (more a rule-of-thumb), but when I run into this type of thing I usually just move the leftover files to another (temp) folder.
If nothing complains imediately, then they're not currently loaded (good sign).
Reboot and check for related errors.
Depending on the situation I may sit on the (to-be-deleted) temp folder for X time period before actually dumping it.
*Shrug* Just a Thought...