Missing mail messages after upgrading

This morning my iMac asked me to upgrade to the latest Mail version and convert my existing messages.  After doing so, I seem to be missing emails from present day back to May 2011.  I am running OS 10.6.8, Mail V4.6 (1085). Ideas?

Will it possible to recover the messges?
Yes, but I'm not sure what your problem really is, though.
First of all, just restoring the HOME/Library/Mail folder is not enough, you should have restored the HOME/Library/Preferences/com.apple.mail.plist preferences file as well. This file is where most preferences and all account settings are stored.
As to the "Message has not been downloaded from the server. You need to take this account online in order to download it." error message, this is one of the many bogus error messages in Mail that have absolutely nothing to do with what the issue really is. The real problem isn't related to not being "online" at all, but rather with "overstuffed" mailbox issues, or with failed conversion from Mail 1.x, or both.
You shouldn't have experienced this problem as a consequence of just moving from one machine to another with the same version of Mac OS X, however, which is what makes me believe you didn't restore your mail data properly. If you haven't received and/or sent mail using the new machine yet, or if what you've sent/received is still on the server, I'd suggest trying to properly copy again both the preferences file and the Mail folder to the new machine. Do this while logged in as the user that's going to use those files in the new machine to avoid possible permissions issues.

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