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Missing software from DB folders

Over Christmas we had a problem with our 3.6.1 server where nearly all of the folders in C:\Program Files\McAfee\ePO\3.6.1\DB 'diappeared'. After restoring these (by checking the packages in again), everything was fine. However, the same thing has happened again last night.

I really have no idea what this could be or where to look (there doesnt appear to be anything obvious in the log files).

Any ideas?