Ok, this was a bit of a sledgehammer, but here is what I did. The idea was that the indexes were corrupted, so delete them and let Yosemite rebuild the indexes without being confused by the existing indexes. As you may know, the mail data is in ~/Library/Mail. So, I made a copy to ~/Library/MailBackup as I experimented with different options. "Envelope Index-*" are built by the import, and increase with every failed attempt, so certainly they could be deleted. I deleted every *.plist, presuming Mail would rebuild them. Ditto *.backup. AvailableFeeds, DefaultCounts, Metadata, RSS, *.noindex were deleted on general principles.
The real problem I suspect was in *.mbox, which was the old Mail format. Our mail when we checked it in 10.6.8 had some blank emails (who checks 4 year old emails for integrity?...). Where did they go? Who knows, but I suspect that was the real problem. So, I deleted *.mbox. Now restarted Mail, and the import worked this time. We lost a few emails from 4 years ago, which was probably when we made the last transition.
Hope that helps!