Hmm... well PlecoDict can only access one flashcard file at a time, so if the modification dates are getting updated that's only because PlecoDict is opening some of the files and immediately closing them (due to file corruption or some other issue). So it might be a good idea to figure out which of the two remaining flshcard files is actually getting used and disable the other one. Try renaming one of them to some extension other than .peb and see if PlecoDict still has all of the flashcard lists intact; if so, you can delete the renamed file, if not, change its name back and rename the other file.
The User DBs are a different story, you can potentially have more than one of those open at once (the reason you have so many of them is because of a bug in Beta 2) so it's possible you might have entries spread across all of them. Try tap-holding on the dictionary switching button and selecting each of the user DBs in turn; some of them are probably empty, so if you repeat that renaming procedure you can find the ones that are empty and get rid of them.
Anyway, we fixed the multiple User DB bug in Beta 3 and we think we've nailed the bug that can corrupt flashcard data files for version 1.0, so once you get this sorted out you (hopefully) won't have more problems later.
The User DBs are a different story, you can potentially have more than one of those open at once (the reason you have so many of them is because of a bug in Beta 2) so it's possible you might have entries spread across all of them. Try tap-holding on the dictionary switching button and selecting each of the user DBs in turn; some of them are probably empty, so if you repeat that renaming procedure you can find the ones that are empty and get rid of them.
Anyway, we fixed the multiple User DB bug in Beta 3 and we think we've nailed the bug that can corrupt flashcard data files for version 1.0, so once you get this sorted out you (hopefully) won't have more problems later.