Thank you so much for the detailed response, Brian.
I noticed another recent thread around the same problem:
http://forums.omnigroup.com/showthread.php?t=14317
I double checked and all my versions are up to date. Also, I noticed that Compact Database under the File menu is disabled, not that I ever do it manually, so I think I can rule that out as what is causing it?
As a precaution for now, based on what I read in the other thread and your response, I
disabled auto-sync on the phone. I'm hoping that now I can be sure I'm never changing the database while the phone is syncing.
Thanks for the help! If it happens again I'll send in my sync database for analysis, but I'm confident you guys will be able to fix any of these problems in a future update as always!