My dotMac mailboxes are duplicated - how can I delete the duplicates?

I see that problems rather like this have appeared in this forum but mine doesn't seem to be quite the same. I have two locations each with a Mac running Tiger (now 10.4.9) and I have a .mac account: I use Mac Mail as a mail client. One of my machines had an unrecoverable disk crash and the HD had to be replaced. I then reloaded Tiger and did all the updates etc, and then tried to recover my mail: I only tried to recover my .Mac mail, not my other POP accounts to start with. This worked. Then I went on to re-introduce my POP accounts from other ISPs (I have a number of these). I made some mistake in the way I chose to Sync the .Mac mail (I think I chose 'merge'). The mailboxes looked fine on my recovered system, but when I went to my other location and started up Mail, I got two copies of the whole .mac mail system - all the mailboxes and messages shown in the left column of Mail. There doesn't seem to be any way of deleting one of the copies. I also get copies of the POP accounts, and if I try to modify one of them in the Mail Preferences Accounts pane (so as to disable the 'shadow' account for example), I get messages like
"Invalid Directory
The account path /Users/graham/Library/Mail/[email protected] is already being used by the account "XYZ at Blueyonder" "
(I have modified the user name for privacy reasons).
How can I restore stuff to normal, an in particular how can I safely get my mailboxes back to a single representation of each one? I should say that I'm also getting the dreaded duplicate mails problem, but I would like to tackle one issue at a time.

You’re welcome.
You should also be able to fix the problem on the current location by re-creating the file where account settings are stored and resetting sync data in the opposite direction:
1. If you have a .Mac account and .Mac synchronization of Mail data is enabled either in Mail > Preferences > General or in System Preferences > .Mac, disable it before proceeding.
2. Quit Mail if it’s running.
3. Make a backup copy of the ~/Library/Mail folder, just in case something 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 locally stored.
4. In the Finder, go to ~/Library/Preferences/. Locate com.apple.mail.plist and move it to the Desktop (to be deleted if this fixes the problem).
5. 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.
6. You’ll 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.
7. You may also need to re-install or re-enable any Mail plug-ins you have installed for Mail to recognize them.
8. 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.
9. If the problem is fixed now and .Mac synchronization of Mail data was enabled at the beginning, enable it again, go to System Preferences > .Mac > Advanced, click Reset Sync Data, and choose the appropriate options to reset the Mail data stored on the .Mac server with the data locally stored on the computer, i.e. sync data must flow from the computer to the .Mac server.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder. You can easily locate any of the folders referred to in this post by copying the folder path here, doing Go > Go to Folder in the Finder, and pasting the folder path there.

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