If you notice (even after deleting lots of mail files) that your main Thunderbird profile folder is still bloated. Check out this post on the MozillaZine Forums. Basically if you run File>Compact on a specific folder (while in Thunderbird) it will permanently remove your deleted files and it will bring your profile folder’s size down.
I like a small compact folder because I zip up the specific profile folder, and upload it for safe keeping onto my storage web site.
Here are a couple more posts on the subject as well: * viewtopic-27849 * viewtopic-15668
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