Duplicate mailboxes and deleted mail archive

Question

So after installing the latest Mac security update, Security Update 2006-007 PowerPC (no idea if this is related to the problem or not), Mail 2.1 was not able to receive messages from my POP earthlink account, even though I could check it through my browser, so the internet connection was not the problem. Everything looked the same in the Mail preferences, so I decided to run Earthlink Total Access and use it to 'set up Mail for my account' in case anything had changed that I wouldn't know about. It said Mail was already configured for the account and when I relaunched Mail there were now two listings of my same email account - one with all my old messages and one that was 'new' and empty and both now received a new email at the same time. Naturally, I found it displeasing to have two copies of one account showing, so I tried to delete the new copy. I can't remember if I tried to delete this duplicate mailbox through the preferences or by right-clicking on it in the left hand column. Anyway, both boxes are still there and they still work, but all my old messages are gone - except for sent messages. Mail still lists all the subject lines, but instead of the actual contents, clicking on them shows this message:
"The message from ____ <________@________.com> concerning “___” has not been downloaded from the server. You need to take this account online in order to download it."
I hope there's a backup copy somewhere of these messages. [I already ran FileSalvage and it did not turn up any.] Oh, they don't show up in Spotlight anymore, either. If Mail itself doesn't keep an archive, is there a way to look at recently trashed items on the hard drive and recover them? I suppose I'll need to do this before I write new data to the disk, so please respond quickly. [Maybe I overwrote them when I downloaded FileSalvage....]
OK, so accepting that all the old emails are gone forever, I still have these very important questions about the application:
How do I re-download the emails that are still on the server? I have emails going back to Nov. 9th that I can access through a browser, but I'd like to at least get those onto my HD.
Also, I can't save any changes to either copy of the same account because I get a message that says I already have an account with the same name. I still need to delete that stupid duplicate, but I'm afraid to mess with it until I know for sure that there's no way to get my emails back. Right now one mailbox preference window says it deletes downloaded messages after one week and another says it deletes after one month, but I don't want anything deleted from the server, but I can't change the settings, as noted.
Can I automatically backup my emails to a more secure location or change Mail to not erase things so easily?

Answer 1

The other messages are lost, then. If you don’t have a backup and FileSalvage cannot recover them, you’re left with whatever remains at the server. Unless you want to continue trying to recover deleted *.emlx files, proceed as follows.
For POP accounts, Mail uses a file within the account folder to keep track of which messages have already been downloaded. Deleting that file causes Mail to treat everything still on the server as if new and try to download it again:
1. Quit Mail if it’s running.
2. In the Finder, go to ~/Library/Mail/POP-username@mailserver/.
3. Locate one or two files named MessageUidsAlreadyDownloaded and move them to the Trash. Mail 1.x used MessageUidsAlreadyDownloaded to keep track of which messages had already been downloaded. Mail 2.x uses MessageUidsAlreadyDownloaded2 for the same purpose.
Before opening Mail again, re-create the preferences file to get rid of the duplicate account settings without also deleting the account folder (ignore step 1, I’m just copying & pasting here):
1. Quit Mail if it’s running.
2. Make a backup copy of the ~/Library/Mail folder, just in case something else goes wrong while trying to solve the problem. You can do this in the Finder by dragging the folder to the Desktop while holding the Option (Alt) key down, for example. This is where all your mail is stored.
3. In the Finder, go to ~/Library/Preferences/. Locate com.apple.mail.plist and move it to the Desktop (to be deleted after fixing the problem).
4. Open Mail. You’ll have to set up your non-.Mac accounts from scratch all over again. If given the option to import existing mailboxes or something like that, don’t. Just enter the account information and Mail will automagically rediscover the data in ~/Library/Mail/ when done.
You’ll also have to re-configure most of your settings in Mail > Preferences. For spam-related security reasons, the first thing you should do is go to Preferences > Viewing and disable Display remote images in HTML messages if it’s enabled.
5. As a side effect of re-creating com.apple.mail.plist, Mail might rename Outbox (which is where messages waiting to be sent are stored) to Delivered. The name of that mailbox is actually a misnomer, as it would contain messages (if any) that couldn’t be delivered for some reason. You can delete that mailbox if you wish.