Missing emails after Software Update

Hi all,
I seem to missing a large chunk of emails in my Inbox after a recent Software Update. This is only in my Inbox. My Sent mail seems fine. Before the update, my Inbox had around 8000 emails. Now it hovers around 600.
I looked at my Home>Library>Mail>Mailboxes folder. There, it says the size is 110 MB and was last modified on today's date. That tells me all 8000+ emails are still in there, but they just aren't being displayed. I tried Rebuilding the mailbox a while back, but that offered no solution.
Any advice?
Many thanks,
Jon

Try these directions
http://support.apple.com/kb/TS1967
Except in step 7, I recommend copy & pasting instead of dragging.

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