Why would my Inbox suddenly be empty?

Hi -

Tuesday morning (9/22) my Mail (on my MacBookPro) was empty meaning that about 800 Received messages and countless Sent had vanished. Mail was displaying a dialog box to set up a new account (Yahoo, iCloud, Google, AOL, Other). Does this mean my account was deleted along with all my messages?

Since then I have gotten Mail running correctly again but the messages are still gone. I've been reading about recovering them from Time Machine but my big concern is why would this happen?

Does Mail have a limit on the number of messages it will store?

Has there been a bug, virus or something nefarious I should be routing out?

I get email via a Webmail account with GoDaddy (they admit nothing) and THAT webmail account also suffered. Is Godaddy the source of my Apple Mail account being deleted?

I update whenever OS X alerts me to. Could that be the cause of this?