Is it possible to do the stuff suggested above and then save the cleaned-up file over the template as a new one?
Another possibility is to have that and an empty new drawing (fully scrubbed first) open side by side. Then you can copy the elements a few at a time to see at which point the bad layer returns (I take it that's when you reopen the drawing? Then that's what you may have to do with the empty drawing). it might be tedious, but at least you may be able to track down the offending element(s) and look further into fixing them individually :-)
I hope my info was useful, but if by some odd chance it actually solved your issue, feel free to mark your post as "Accept as Solution". Thanks!