The easiest (IMHO) would be to note which omod that was the owner of the overwritten resources, and then deactivate+activate that omod afterwards, to get its files back.
I was thinking of that method too. It does not seem to be such an disadvantage then. You just switch between the two OMODs. Of course, if your OMOD starts to overwrite files of several other OMOD things get more complicated. But I think this won`t be the case, because I won`t use a lot of mods and nothing complex like FCOM.
Thank you for all the replies.