Sorry for the delay. I think either...

1) add a way of customizing the indexer to specify the function to use to check if a file should be scanned.
2) use your suggestion of just resetting the last scan time on each track

First suggestion is probably quite a bit of work, and would be best as a PR in itself.  And 2 is easier...  your call, I'm ok with either as long as it's well tested.