Mac Mail Emails Vanishing

I had a client that recently wiped his OS X mail server while attempting to upgrade to Mavericks. I Was able to get the email accounts setup (none of the previous emails were backed up). Authenticating all the Windows machines worked perfectly; however, once I re-authenticated the mac mail accounts all the users old email disappeared. I navigated to ~/Library/Mail/V2 and there was only one inbox file and it was only about 25MB so I have no idea where the email went if it just disappeared. Is there any way for me to get the mail back? I am running out of ideas.
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Eoin OSullivanConsultantCommented:
You are correct that ~/Library/Mail/V2 is where all the emails should be stored for that user.  Apple Mail has an aggressive policy of DELETING or OVERWRITING mailboxes in that folder when accounts are changed - which has caused heartache for many users in the past.

Your ONLY real hopes are
1. IF you have timemachine or another backup of the desktop mac which pre-dates the mail problem you could restore that ~/Library/Mail/V2 folder contents and rebuild the mailbox.  If this exists we can provide further steps.
2. You can TRY and use a data recovery program such as Stellar - but to be honest it is likely that email data recovery will only be partial unless the HD has had very few edits and plenty of free space to minimise the overwriting of deleted data.

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