Right now it skips that file as a duplicate -- are you saying you want the old tune to be removed and the new one to take it's place instead?

Exactly. Why else would I have a different version of the same song on my PC unless I was fixing a bad rip?

For tune-duplicate-checking, the tag information combined with file size is plenty. But if the actual bits are different, then you know you re-ripped the tune.

When you talk about doing soundprint signatures, that would identify the song, but not whether it was a re-rip. Two different rips would appear (correctly) to be the same to a soundprint signature.

And what about not just re-ripping, but upgrading the bit rate too? Say I've got an album at 128 on my player and on my PC. Then I re-rip at 256 and copy over those files on the PC, then drop them onto the soup. It should say, "ah, cool, this is a new rip" and replace all the FIDs.