Thus, the best bet is to make a copy of the items in the quarantine directory, writing them to a USB token that...
has no other legitimate use (make sure it's not one of those auto-executing U3 USB devices). Then, clear out the quarantine folder. Keep in mind that it could take weeks for a user to know if the items that were quarantined were useful for an application on the machine. A problem would only manifest itself when a legit app requires an esoteric DLL or even an EXE that has been deleted. Thus, hold onto the contents of the USB token for a about a month before finally deleting it thoroughly. This process, although cumbersome, is the safest way to empty a quarantine folder.
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