Um...let's roll this all back to the original issue.
I'm guessing there is corruption in the Mail folders somewhere. So there are various things that should be tried - not sure why this hasn't been suggested yet, as it's usually the place to start with mail issues.
Obviously, do a cloned (preferably) backup before starting any of this.
Solution 1. Rebuild your accounts. This could take a while if you've got a lot of mail.
1. Launch the Apple Mail application on your device.
2. From the list of folders, select the folder that you wish to rebuild.
3. Click the Mailbox menu followed by Rebuild.
4. Check if the issue is resolved. If not, try the next solution.
Solution 2: Restoring Apple Mail AccountStep 1:
You can restore your Apple Mail account using the Preferences option.
Step 2:
On your Mac Mail application screen, click the Mail menu.
Step 3:
Go to the Preferences option.
Step 4:
In the window that opens next, select the Account option.
Step 5:
Disable and again select the Enable this account option.
Step 6:
Finally, click the Save button.
Step 7:
Now, check if the Mac mail mailboxes disappeared issue is resolved.
(I doubt that solution #2 will do anything, but hey, worth a try as it's painless)
Solution 3. Reindex your Apple MailboxRebuilding your Mailboxes is often enough to solve many of the issues an overburdened Mail app may experience. However, if you’re still having problems (such as the app becoming so unresponsive it barely works or fails to launch), you should manually reindex your Mailboxes.
Here’s how to manually reindex your Mailbox:
1. Quit Apple Mail if the app is running.
2. Launch Finder and select Go from the Menu Bar.
3. Enter ~/Library/Mail/ and press Go.
4. Choose the V8 folder (depending on your macOS version, it can be named V5, V6, or V7) > MailData. Next, locate and delete all the files that start with Envelope Index, such as “Envelope Index” or “Envelope Index-wal.”
Note: It’s a good idea to copy each file to your desktop before deleting it.
5. Launch Apple Mail. The next time you open Mail, it will build entirely new Envelope Index files. You may have to be patient—this process can take a while if you have a lot of messages for Mail to go through. If everything is now working normally, you can safely delete the old envelope files you'd dragged to the desktop.