Mail present in Mailbox, not showing in Smart Mailbox

OK, this is a bit complicated to explain, but let's try.
To archive old emails, I use to create a Smart Mailbox with criteria, for example, all emails (received or sent) from 01/01/2001 to 31/12/2001.
Then I drag them in a separate mailbox, which I can archive.
As a check, I show on the mail browser the "mailbox" column.
And many mails are reported as "blank" in the Mailbox column.
Worse, when I try to open them, they appear blank, too. No headers, no contents.
But if I do a Spotlight search on the title shown in the browser, I can find the .emlx file, and open it with Text Wrangler. Text Wrangler then give me the path of the file ... which is in the adequate mailbox !! And if I open the file through the result window of Spotlight, Mail decently opens the message ...
Rebuilding the mailboxes doesn't help.
It happens with "small" years (+/- 2000 messages) as well as with "big" years (10,000 messages and above).
Is there a way to rebuild a complete index of Mail ?
Thanks in advance

Claude,
It would appear that you do need to force reindexing. Since forcing reindexing involves more than those On My Mac mailboxes, the issue of what type of accounts you use remains relevant?
To force Mail to reindex, you quit Mail, and in the Finder open Home/Library/Mail and locate the Envelope Index file (hopefully you only find one file with similar name). Drag out, or delete the Envelope Index file from the Mail folder, and then relaunch Mail, which will announce that it is ready to import mailboxes, but really will only set about to index all mailboxes.
Again, if you have anything other than POP accounts, please report that, and if you understand what you are supposed to do with the account folder for non-POP accounts?
Ernie

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Besides, I recommend you mail disable the public folder and then mail enable it again to check the result in the Public Folder Management Console.
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