OSX Apple Mail

I'm doing technical support for someone and have run acrossed something quite odd. After the usual googling and finding others with this issue I am going to re-open this as a new thread.
Apple Mail, Version 6.5 (OSX 10.8.4)
My client has a LOT of email, always been using Apple Mail going back to 10.2. His email about a month or so ago started this thing where he files all of his sent mail in unique folders by client "On My Mac". Any mail he has SENT and filed only appears to be retaining Mail as of the last 30 days though. When I open the Mail Folder, it shows about 224 messages. When I open the exact same thing in Time Machine, And look at TODAY and not going back, it jumps up to 350 or so messages now showing me all of the sent mail that he has also filed in this folder. It only shows me these mails in Time Machine and does not give me an option to restore them either.
So in all, any old mail that was sent appears to be there according to Time Machine, but when I pop back out into Mail, all of his filed sent emails disappear! I know they're there because I can look at them and read them in Time Machine, but the second I drop back out, zip gone.
Any ideas?
I've tried exporting the Mailbox (mbox) and that does not do anything or change anything either.

Hi.
So, just to clarify: your client, after sending an email to one of his own client, goes into the "Sent" folder and manually drags-and-drops the copy of the email he's just sent into a new folder, a folder residing under the section, "On my Mac"?  Or does he have some system of rules set up to perform this automatically?
I recently copied all my emails from a defunct IMAP provider to folders, "On my Mac", and one thing I find is that when I open those local folders they frequently appear to be empty.  If I re-launch Mail and check again, the emails re-appear (though not always).  This appears to be a bug of some sort, as I have witnessed the behaviour on two different Macs.  Is it possible your clients problem is similar to this one?  That is, the emails are there, but are simply not being displayed?
As a troubleshooting measure, you could have your client archive his sent messages with MailSteward.  It's free until you archive over a certain number of messages, so should suffice for this purpose.  If you find that the messages appear in MailSteward, it's likely that the mboxes do contain all the messages your client has filed, but Mail is simply failing to display them.

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