A couple days ago I did a clean install of 10.3 on my iBook, then installed DEVONthink 1.7.3 and ran it without the original 1.7.2 database from 10.2. Later I copied the ~/Library/Application Support/DEVONthink directory from 10.2, but not all of the other directories which had been a source for DT content.
At first everything looked okay, then yesterday I noticed some of the links are botched in a few ways: some are no longer in outline mode and several have randomly peculiar pathnames (e.g. one references a file under ~/.cpan, which shouldn’t have any connection with DT). Also, one search I do matches content added after the migration which Reveal can’t find (Info shows it has no Name).
So far it looks like only links have bogus paths while other content still refers to paths from the original 10.2 system. And all the actual content looks okay, too. I haven’t rebooted with 10.2 to look at the old database for comparison since that would be a hassle with only a single machine.
Verify & Repair claimed "No errors found". I also ran "Backup & Optimize" this morning after creating an archive of the database directory.
I’m still running DT unlicensed and my database is relatively small. Now that I’ve upgraded to Panther I hope to license and use DT more seriously, especially with the improved RTFD clipping (as Bill DeVille described in another post, which was part of my motivation for upgrading to Panther now 
). First, however, it’s crucial that I can clone and move the database without this sort of trouble since I intend to eventually move it off my iBook to a new system within the next couple months.
Have I discovered a DT bug or was there something amiss with how I did the database migration? If necessary, I can remove everything DT-related from 10.3 and replicate the same migration steps since I still have the original database on my 10.2 partition. I’ve already considered doing that to see the results are but I wanted to report this before anything else.
Thanks for any feedback.