I have a problem like this too. I ended up importing hundreds of files and converting them to DNG in LR. I clicked on the "new photos" rather than the "all" button on the import dialogue and ended up with all anyway. I deliberatley did not choose the don't import suspected dupes option because camera counters can roll over the same file number sometimes.
Now I have up to 5 dupes in some cases with extensions of -1 -2 -3 etc., on the same basic file number.
I'm on Windows 7. Anyone know of a PC based package that might do this? Thanks.