[dnanian]

I usually suggest that when you move to a major OS version, it's a good idea to do an erase-then-copy. So much content has changed that you'll end up with a much more fragmented volume (zillions of small file deletes, moves and copies).

But I don't know of anything in Smart Update that would be "confused" just because a lot of files changed. OS X might be playing some games there, though - or, one of the files on the drive might have had some bitrot and was "up to date" but its content might not have been correct.

Remember - bitrot can occur. It's always a good idea to have multiple backups of stuff...