Lost messages in 3.5 upgrade

Greetings,
I just updated OSX and mail, and when I the machine booted back up, mail gave a message that it had to update IMAP settings for ToDo lists (or something like that), being completely lost as to what it meant I hit OK. Once I did, all my e-mails were gone.
Is there a way to get these back, or are they gone as if I had deleted the account? If they are gone, is there a way to force mail to download the e-mails from the server, as the server still has them (I can read them via web mail).
Thanks!

Well, when I re-opened mail it began downloading 3100 e-mails, so it looks like I solved it.

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