Suddenly all my top-level folders have disappeared from Apple Mail. The “All Inboxes” and the subfolder inboxes are just gone. Any idea how to restore them? There is nothing above “Smart Mailboxes”. Running Big Sur on a 2014 MacBook Pro.
I’m going to assume you’ve already restarted your machine? Otherwise, what email accounts are you using? If it’s something cloud like IMAP, gmail, exchange, and icloud, then I would check your System preferences - internet accounts. Maybe consider disabling the email and then re-enable to see if they will download.
The first thing I do when troubleshooting email problems is log in via webmail. If your folders are there, continue your troubleshooting. If not, you’ll need to restore from backup.