Mail deleted all of my POP3 account mailboxes

So I woke up yesterday to find that 2 email accounts (POP3 accounts), their mailboxes and all of their messages gone in Mail.app Version 3.6.
My Mobile Me account is the only mailbox that is still there. The missing accounts are still synced on my iPhone though. So I've been emailing from that the past day.
Does anyone know what happened here?
I have Time Machine running, perhaps if it's a preference file or something I can restore it from the backup?
I'm a little freaked out because the 2 email accts that disappeared are for my freelance business and have a lot of important info in them. So, in addition to setting up the accts again, I need to recover the stored messages in those mailboxes.
Any help would be greatly appreciated!

Restore the com.apple.mail.plist file, after checking at Home/Library/Mail that the two POP Account folders are present. Quit Mail before restoring the file, btw, then relaunch. Probably only the preference file got overwritten for some reason, but since MobileMe is also in System Preferences, it was automatically restored.
Did anything happen to interrupt Mail's completion of housekeeping tasks, or did free disk space get low for some reason. How much free disk space do you have the hard drive, or if partitioned, on the boot partition? If a lot, would you have been using any video or audio apps that temporarily use lots of space?
Ernie

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Greetings,
Shutting down the computer while Mail was running may have damaged the mail plist where all your settings are stored.
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It is not the kind of sync I am looking for or I am expecting...
If I store an e-mail from one of my POP3 accounts starting from the Hub surface (total view of all events/inboxes) I can see that short tree of four elements (inbox, sent...). But I cannot find it if I would like to re-open my inbox of a POP3 account like I can do it with an IMAP account.
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