Mail (El Capitan) Godaddy IMAP problem after manual migration: STUMPED!

Hi,

I have a fascinating situation which has stumped Apple Support. I realize I'm probably at fault for trying to manually migrate my mail, but it ALMOST worked. If I can fix this one issue I'm golden…

This all started because I needed to do a clean install of El Capitan. Before installing, I cloned my drive using Carbon Copy Cloner (I had a bad Time Machine experience and no longer trust it).

IMPORTANT NOTE: I was already running El Capitan before the clone/reinstall so I’m not switching OS’es. Mail worked fine for me in El Capitan before I tried the migration.

Then I tried to manually migrate my Mail over, but discovered it's not as easy in El Capitan as it was in previous versions of Mail. I ended up using a technique I found on this forum (see apple_mikey’s comment) except I didn’t copy over the ~/Library/Keychains folder because the iCloud keychain seems to be working for me: https://discussions.apple.com/thread/7312611?start=0&tstart=0

So everything worked great with one exception. I have one GoDaddy IMAP account that keeps re-downloading all of the messages. What’s interesting is I have several Godaddy IMAP accounts and this only happens with the one account (although it’s probably the largest one).

Also, the problematic IMAP account works fine on my other machine (running an older OS), my phone, and via the browser app. It’s just on my MBA where it has this problem.

Here is what I tried so far:

- Rebuilding using Mailbox>Rebuild.

- Rebuilding using the method suggested on the same thread linked above (deleting the "Envelope index" files).

- Safe boot: problem persists.

- Created a new user on the same computer and setup the email… problem persists with the new user.

- Called Apple Support. Did a screen share with a tier-2 tech who witnessed the problem. He took some logs from my computer and sent them to Apple’s engineers. That was almost two weeks ago and they are still stumped.

I’m looking for any insight or ideas about how I can fix this.

In a worst-case scenario I am considering another clean install, but this time I will try exporting/importing my local mailboxes. I’d rather not do that if I can help it because it will be a little complicated since I’ve been working on the computer for the last two weeks. However, I’m worried I monkeyed around in my system too much and my only choice is to start from scratch again.

Any guidance is greatly appreciated! Thanks!