Emails with no folder and missing message

This is a problem that has stumped tech support at the product specialist level for several months.
I have many emails that I can find when I do a search BUT they are no longer assigned to the inbox or folder and have lost their content. In the search window I an see the from/to/subject/date/time but when I open the email there is the subject at the top of a blank window. This is happening on my MacPro and my MacBook Pro.
Any ideas?
Thanks,
Jeffrey

Every piece of mail in Mail is in some sort of mailbox. The mail I'm talking about is no longer assigned to any mailbox that I can tell. I can only see these problem emails after a search of All Mailboxes. Looking at the individual mail boxes they do not show up and are not included in the individual mailbox count. I have 3 POP accounts and 1 IMAP. From what I can guess the problem is with my primary POP account.
Anyway, I followed the instructions in the link on your post and the same thing happened when I did this a couple of months ago on my Mac Pro. It reindexed everything and I lost all the problem emails. Contract updates, special client offers, etc.. Since my Mac Pro Mail did this I have been freaked out since I have no control when an email just disappears into limbo-land. Unfortunately my habit of thinking my emails will stay in my mailboxes forever is no longer valid.
I appreciate your insights, they should have worked but once an email has lost it's mailbox and content it seems there is no way to get it back. The odd thing is it happened on both my computers and their only relationship is Mobile Me and Back to my Mac. I have my POP servers set to leave messages on the server after they have been picked up. This problem will continue because my MacPro already has emails that keep falling in this hole after the last 150+ were purged.

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