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Your reported case of a renamed file replacing a different one can only happen when you a got an old zipfile and the new datfile says: delete one (otherwise you got a circular rename) and rename one to that deleted one's name. Pretty uncommon unless the datfile author is a weirdo 8). But then the unneeded check would detect the unneeded one first and moves it to backup, so again, nothing gets overwritten.
So I guess you didn't keep all check/fix options enabled. Send me a repeatable example.
 Roman Scherzer
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