Interesting reading the responses. I don't have anything else that I feel is worthwhile to add, so that's why I am not responding to the followups. In any event, there are a few points to ponder.
My c-client sync script is halfway done, but I quickly realized as I started to code that it has the potential to destroy my inbox if I match one list to another incorrectly, so I'm leaving what I've done for now to mull over it a little more. I wish Palm's developer zone had information on how the MailDB file is structured, but they don't seem to for some odd reason, just some generic stuff on databases. I find that extremely strange, especially since pdbdump from the Coldsync Palm libs shows there is a field called "id" in each message that I think I can use safely.