I can't be certain without the exact text from the dialog, but it sounds like you may be experiencing an out of sync local cache. If so, here's what's happening. Outlook connects to Exchange, which checks your local cache to see what needs to be updated. If it sees mail in your local cache that appears to be newer than what it has, it assumes that the server side copy of your inbox is out of date. In order to prevent itself from overwriting the mail on your client that it does not have on the server, it presents you with that choice.
Again, you may be having a different issue, but if not, the easiest resolution is:
- create a new archive/personal file in Outlook (a new .pst)
- copy your inbox to the new file
- close Outlook
- delete your .ost file
When you next launch Outlook, it will create a new cached copy of your inbox (a new ost, synched from the server). You can then compare contents to see what, if anything, was missing from the server. Copy the necessary messages from the PST to the OST (which will send them up to the server copy), and you can then safely remove & delete the PST you created.