Post-Time Machine Recovery, no emails in folders

I just had to replace my internal hard drive after it crashed, but everything was fine because I use Time Machine. So I load it all back up, and aside from some minor things (Safari 3 needs to be updated again, etc), everything is good.
However, I don't seem to have any emails in folders anymore... Is there a way to get them back? That's a pretty big thing for Time Machine not to back up... Any tips?

It's in Mailbox>Rebuild

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