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EXmerge reported mailbox size is smaller than mailbox size in exchange system manager

Ok a SBS 2003 server died.  I had a backup of the exchange mdbdata folders.  So after remaking the domain and such I replaced the .edb files on the new install with my backup ones.  However there are e-mails in the new .edb data files.  I downloaded exmerge to try and merge the e-mails.  However exmerge reports the size of the mailboxes to be very small.  In the system manager some of the mailboxes are hundreds of megabytes in exmerge they are only a few kilobytes.  There are only e-mail from earlier than today in the .pst that exmerge creates.  
SBSWindows Server 2003Exchange

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Well I kinda figured out what was going on.  Exhange had overridden my backup database with its own.  The small mailbox sizes where from the new mailboxes I created earlier today.
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Everything must be the same.  It has to be the same server name, same database file name, etc.
Since you created a whole new domain and server you can't restore the old backup to a recovery storage group and exmerge it.  The new server will not have the 1:1 mailbox to mailbox GUID mapping.

What you may be able to do is restore the old database (hope it was an Exchange-aware restore) to a recovery storage group.  Run the eseutil /cc to replay the transaction logs from the incrementals and run eseutil /mh to ensure that the database/store shut down cleanly.  If it shows a dirty shutfown run eseutil /p and isinteg -fix to repair the database as noted in the Exchange 2003 DROPs guide (link below).

This is a very high level checklist.
Make proper notifications through whatever change management procedures you have in place.
Perform a backup of the server, using an Exchange-aware backup.
Restore the backup containing the old .edb to a recovery storage group and recovery mailbox store.
Mount the store in the RSG.  If you can merge the mailbox data then great (likely you will not be able to do so).
Dismount the RSG.
Make a backup of the existing mailbox store.
Exmerge the existing mailbox store.
Dismount the existing mailbox store.
Rename the existing mailbox store (temporarily)
Copy the RSG files to the existing mailbox store.  The file names must be the same as what the existing mailbox store was named.
Mount the store that was the old mailbox store.
Run the cleanup agent if the store mounts.
Re-attach the mailboxes to the user accounts.
Exmerge in the old data.

Another option to recover the data would be to utilize a third party product such as those from Quest or Ontrack.  I have used both tools to perform a recovery, Quest a few months ago and OnTrack a few years ago.
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Figured it out.

Exchange is the server side of a collaborative application product that is part of the Microsoft Server infrastructure. Exchange's major features include email, calendaring, contacts and tasks, support for mobile and web-based access to information, and support for data storage.

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