Strange thing this morning, on my main account (Fastmail, IMAP) Apple Mail doesn’t show any of my folders except Inbox and Trash. I logged into Fastmail and they are there. I have been playing with Thunderbird recently so I fired that up and all my folders showed up.
In apple mail I have tried Disable/Enable for the account, Synchronize Mailbox. I also went into CleanMyMac and told it to reindex. Folders just don’t show up.
Anybody see this? Any thoughts or suggestions? Thanks.
Yeah… Apple Mail… IMAP… And its database…
If this does not help: delete the account in Apple Mail, delete the data on your disc. Set it up as a new account in Apple Mail.
Or use a tool like Onyx (I never have tested it with Onyx):
The tool also has the option to delete the “mail index” and to create a fresh one afterwards.
Thanks. I might try Onyx (I run it periodically anyway).
That didn’t do it. 
I ran onyx and had it delete the indices so that Mail had to rebuild all of them when the system restarted. Same problem. This is really weird.
Turns out that Fastmail had made a change that affected accounts with 2FA. I was able to fix my iMac by removing the account completely and re-adding it. Fastmail, however, made some change to my account so that on my MBP I just had to quit Mail and restart it.
I am back to normal now.