Chunks of In Box mail gone after upgrading from 10.3. to 10.4

Question

I have a client that "lost" a chunk of Apple Mail emails (only from the In Box) after an Archive and Install from Panther to Tiger (10.3.9 to 10.4.9). We did a rebuild. No love. Sent emails exist but that inbox is decimated. It's receiving mail fine but past mail? Nada.
The one account is POP.

Answer 1

The conversion from Mail 1.x to Mail 2.x is broken. Take a look at the following thread to better understand the problem:
Help! "You need to take this account online in order to download it."
More specifically, if this is a POP account, the following procedure should allow you to fix the Inbox problem. A similar procedure should allow you to fix other mailboxes that might also be affected:
1. Quit Mail if it’s running.
2. Make a backup copy of the ~/Library/Mail folder, just in case something goes wrong while trying to fix the problem. You can do this in the Finder by dragging the folder to the Desktop while holding the Option (Alt) key down, for example. This is where all your mail is stored.
3. Create a new folder on the Desktop and name it however you wish (e.g. Inbox Old). It doesn’t need to have an .mbox extension.
4. In the Finder, go to ~/Library/Mail/POP-username@mailserver/INBOX.mbox/.
5. Move the files mbox and Incoming_Mail out of INBOX.mbox, into the Inbox Old folder just created on the Desktop. These files contain all the messages that were in the mailbox before the upgrade to Tiger, and maybe even some messages that had been deleted. mbox is the most important. Incoming_Mail may or may not be present.
6. Move any strangely-named Messages-T0x... folders to the Desktop (not into the Inbox Old folder). These folders are to be deleted after fixing the problem. They are temporary folders created during an import or an indexing process, and Mail should have deleted them when done. Their presence is a clear indication that something didn’t work as expected. If you’ve been using Mail after the conversion and have already tried to fix the problem by rebuilding the mailbox or something like that, they might contain messages that are neither in Messages proper nor in the mbox file, so keep them around until the problem is fixed.
7. Move everything else within INBOX.mbox, except the Messages folder, to the Trash.
The result of the above should be that INBOX.mbox contains the proper Messages folder only, and the Inbox Old folder on the Desktop contains the mbox and Incoming_Mail (if it exists) files only. Now, proceed as follows:
8. Open Mail.
9. The account’s Inbox should properly display in Mail as many messages as *.emlx files are in ~/Library/Mail/POP-username@mailserver/INBOX.mbox/Messages/. If that’s not the case, select the mailbox in Mail and do Mailbox > Rebuild.
10. In Mail, do File > Import Mailboxes, choose Other as the data format, and follow the instructions to import the Inbox Old folder that’s on the Desktop.
As a result of doing the above, some messages may be duplicated now. Andreas Amann’s Mail Scripts has a Remove Duplicates script that you may find useful.
Do with the imported mail whatever you wish. You may move the messages anywhere you want and get rid of the imported mailboxes afterwards.
If all is well and you don’t miss anything, the files on the Desktop can be deleted, although you may want to keep them for a while, just in case.
Take a look at the following article (also referenced in the thread I mentioned at the beginning of this post) to learn what you might have done before upgrading to minimize the risk of this happening, and what you may do after fixing the problem to avoid similar issues from happening in the future. DON’T do now what the article suggests, though, as that would make things worse in the current situation:
Overstuffed mailbox is unexpectedly empty
Ask for any clarifications or if you need further assistance.
Note: For those not familiarized with the ~/ notation, it refers to the user’s home folder, i.e. ~/Library is the Library folder within the user’s home folder.