How to delete Apple Mail mailbox that only shows in Finder?

Is Roche a subfolder under COMPANIES? Is this an IMAP account? Is it possible you are no longer subscribed to this folder?

I sugget you first try rebuilding Mail's index first to see if it will show the folder in Mail.

With Mail quit....

Go to your User's Library/Mail/V4/Maildata folder and delete the three files with envelope in the name.

Open Mail. It will reindex your files.

If this fails and you can manually remove the folder, you will need to do the reindex again. Anytime you make any changes manually, you would need to reindex Mail.

Be careful that you got just the subfolder and not the parent folder COMPANIES if you do this manually in the Finder.

Always backup first when making changes like this.

I rather would like to fix the issue without rebuilding Mail's index (eg., doing it from Apple Mail), if possible.

How about the Rebuild command in the Mailbox menu. Try selecting all of the account Inboxes and use the Rebuild command. Diane's method does the same thing, but more efficiently.

Are you certain they are still POP? Sierra will convert POP to IMAP if the email provider has that service.

Rebuilding will not take hours. Should be done in a few minutes. It's not like rebuilding in Microsoft's Entourage and Outlook.