Since this thread will end up archived somewhere, I thought I'd add
another person's solution to this problem of Mail breaking after an OS
upgrade, that was sent to me. It's basically what I did myself, but
for anyone who needs to be walked through it, here is his solution,
step-by-step:

"I've encountered this problem on the last three upgrades from Tiger
(10.4.11) to Leopard (10.5.6). I've done three different upgrade paths
(simple upgrade, clean install, erase/install and migrate) and in all
three cases, the Mail problem is exactly the same. When Mail launches,
it says the Mail files need to be updated (or something similar), I
say OK, and after a few minutes it reports that Mail is ready to use,
I say OK and mail opens to a few generic mailboxes with nothing in
them. All the mail seems to be gone. Mail hangs and I have to force
quit. I can't send or receive mail.

Here is what I have learned and what I recommend. If you are reading
this after you've encountered the problem, described skip to step 3.
If you haven't yet done the upgrade start at the beginning.

By way of preview for the steps below; basically, you will document
your current settings, then create a new, empty mail system. Then you
will import your mail and reconstruct your mailbox structure. The
steps below will guide you through this process.

1. Before you upgrade, document all of your email settings for login
and password, server settings for sending and receiving mail. Also
document the arrangement of all of your mailboxes. I recommend making
screenshots (cmd-shift-4 followed by spacebar then mouse-click to
capture an image of the window). Do this for all relevant views of
your mailboxes, so you can see what you want your mailbox structure to
look like after you are done. The pictures will probably land on your
desktop and be named Picture 1, Picture 2 etc.

2. Upgrade your OS normally, do all of your software updates etc, but
DON'T LAUNCH MAIL YET!

3. If Mail is running, make it stop. Trash the file;  /Users/
(yourusername here)/Library/Preferences/com.apple.mail.plist

4. Move the folder;  /Users/(yourusername here)/Library/Mail to the
desktop. This is where all of your email is. DO NOT TRASH THIS FOLDER!

5. Take the computer off the network. You don't want it to check your
mail just yet. Either turn off your Airport, or disconnect your
Ethernet cable, or both.

6. Launch Mail. It will ask you to configure it  for the first time.
Since it is not on the network, you will need to configure it
manually, using the settings you documented in step 1. Don't let it
configure itself, because it is not on the network and will not be
able to find any servers.

7. After mail is configured, you can bring the machine back onto the
network and confirm that your mail settings work. Undo whatever you
did in Step 5.

8. Import your old mail into the new mail settings by choosing
File>Import Mailboxes. Point the import step to the Mail folder on
your desktop that you moved in step 4. NOTE: If you open the Activity
Viewer under the Window menu > Activity, it will let you watch the
subsequent processes, which can take a long time under some
circumstances. Especially if you have a lot of mail, or if you are on
a slow computer.

9. After the mail is imported, it will be in a folder called something
like Imported Mail.

10. Recreate your original mailbox structure by dragging the mail
files (you can select multiple messages) from the folder in the
imported mail to the place you want it, or originally had it. This is
where the screenshots from Step 1 comes in handy. Drag mail from your
imported inbox to the new inbox, etc.

Some mailboxes will not exist yet. If you don't have a "drafts"
folder, for example, create a new message (to anyone - it doesn't even
have to be a real address) and save it as a draft. This will create a
drafts mailbox and you can then drag mail from your imported drafts to
the newly created drafts mailbox. If there is no Trash mailbox, create
a new message and then delete it, this will create a Trash mailbox.
You can create some of the mailboxes from the Mailbox menu > Go To and
choose the mailbox you want. For example, to create the trash folder.
Go to Mailboxes->Go To->Trash  (or command-5) and that will create a
trash folder.

You may need to recreate your rules/filters. You are on your own
there. Maybe document them in step 1 along with the other
documentation you make of your previous setup.

This is a big problem for a lot of people. I've seen it enough to have
figured it out and I documented the steps for fixing it. I hope this
helps."

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