I had similar issues, but wasn't losing any entries. The unknown errors of DM are frustrating at best.
I edited all of my events, removing any all-day events and changing them to 8-8:30 am appointments. I also removed any categories, and any links to other items. I think I messed around with a few other settings that I thought Outlook and DM might choke on, can't remember everything.
I think part of my problem was that I had forwarded several appointments from one Exchange account to another, and therefore there were weird references/senders/owners in and of various appointments.
I only had about 1400 appts to deal with - sounds like you might be in for an afternoon of hacking about in Outlook to get it all sorted.
I've changed my appt entry techniques in order to maintain painless syncs and to avoid this kind of crap in the future.