I did give this a try and it seems to work (again, it doesn't avoid the ingest, just the subsequent culling).
I have the file handling preferences set to append a letter (A, B, C). Since my camera always has digits in the last part of the file name, then anything with a letter there is was a duplicate file name. And at least on Nikons, the file names are the same on backup files (not sure what you are shooting).
So when I ingested a card with a few shots extra on the second card, I got a bunch of files like DD5_5706A.NEF, and could just delete from the command line *A.NEF and what's left are the original files plus those which were incremental to the first disk.