Well, to reiterate-
Compact & Repair is a Jet operations, not a Windows operations, so simply copying & pasting a .mdb via Windows Explorer would do nothing to reduce the size. However, creating a new .mdb and importing all data into the new .mdb could end up with a smaller size because it doesn't import in all "junk" that caused the bloat.
If it's possible someone could have copy & pasted it into a subfolder, then it's not that much bigger leap that the same person could have had C & R'd it.
Can you verify whether the data itself are intact? (e.g. if you have a old report from past, re-generate the same report and see if it still compares to the old report, for instance).