Wow – Today in the midst of keeping up with a array of work responsibilities, my email got completely messed up. Apparently Mail can get a bit finicky if you transfer messages back to the inbox from other folders.
I created a new rule to filter messages based on a client domain and then inadvertently released the track-pad Mail to Transfer again to a folder with my entire inbox selected. Every message was sent to the sub-folder and when I Transferred them back to the inbox they disappeared. No longer visable in my inbox (for any account of 4) or in the transferred folder, I started to panic as I had about 150 messages remaining in my inbox to file at the appropriate time.
I did a search on the Apple boards and came up with seemingly an exact instance of my situation, though the person who posted the problem had gotten there from a different path. I tried a solution there which involved changing the Open with… properties of an Mbox file and importing it into Entourage, to then import it back to Mail. No luck for me. The import in Entourage did not work at all! It did seem to want to import, but no messages ever came in.
I killed the prefs in Mail. This caused me to have to re-create all of my accounts other than my .Mac account which seems to stay (I guess from Internet Prefs). After I did that my solution was to then try and import my messages from the actual existing Mail folders. These are found at User Home/Library/Mail a folder exists for each account and you can import things back to Mail. My problem was that since I had taken some time to arrive at this point (damn panic!) I had already received some new mail in my newly created accounts. In order to maintain the messages I had previously I duplicated the new inbox files and the moved the old files into my new folders. This brought back my history of messages and then I was able to import the copies I had made to bring my newer mail back in.
I should mention one more detail. I also did an import from the root level of my Mail folders in the finder. This caused all BUT the inbox to come back in. Thanks, Apple. Not sure what the inbox folders from previous prefs are the only ones not brought back in, but it is the case. Fortunately I had my wits (at that point anyway) to remember the finder folder structure.