Changed mbox but can't empty trash...

Hi,
Following advice, I've put my Mail directory on an external drive and used an alias on the internal drive to point to it. I then deleted the Mail directory that had been on /Users/me/Library/ but when I try to empty the trash, I get, +impossible to complete the operation: element "Messages-1" is being used+. When I do 'continue', I see the same error for every folder that was previously used by Mail.app.
Anyone know how I can delete these folders? Anyone know why Mac OS-X is telling me that I can't delete 'em? Are they really being used? If and when I finally get rid of them, is Mail.app going to keel over and die on me again (strictly speaking, this shouldn't happen as I have multiple back-ups of the entire Mail directory)?
Oh and a strange thing happened. I logged out and back in and when my session opened, Mail.app opened with the +Welcome to Apple Mail+, but when I hit cancel and then opened Mail.app manually, I got all of my mailboxes back.
Any advice would be welcome. Thanks.

Use "TinkerTool System 1.72" to delete the folders and files.
<http://www.macupdate.com/info.php/id/13662>
-put all the folders and files in one folder on your desktop
-launch TinkerTool System and click on "Files" - then "Force Delete"
-check-mark "Allow deletion of bundle or folder containing files"
Good luck,
Tom

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