If the Junk folder is acting like an Inbox, you can probably fix it with this add-on:

https://addons.thunderbird.net/en-us/thunderbird/addon/folderflags/

https://support.mozilla.org/en-US/questions/1460237

Thanks for your reply. I have installed FolderFlags and the folder in question has two flags; inbox and junk. Which one do I delete please? When I have deleted whichever flag I need to, will I be able to delete this duplicate folder. Likewise can I delete the duplicate BT Internet junk folder.

The Junk folder should only have a junk flag. When TB restarts, there should only be a single (Hotmail) Junk folder.

I don't know why you see duplicates, unless you have both TB's Junk Controls and the mail provider's spam/junk filters enabled. I would employ one or the other, but not both.

I removed the inbox flag and restarted TB. Sure enough the second junk folder has gone. However there is now another problem. In unified folder mode my hotmail inbox folder does not appear with the other 5 inbox folders. Instead the hotmail inbox remains in the hotmail folder - see screenshot. Something is stopping TB moving the hotmail inbox into the unified folders inbox. Any idea how to fix this please?

I think I have sorted the missing inbox in unified view using this thread - https://support.mozilla.org/en-US/questions/1479993 (the 11:37 entry)

A better remedy is to reset unified folders:

https://support.mozilla.org/en-US/questions/1429758

The remedy in the thread you have suggested is the same as the thread I quoted. The problem is solved and I now know for the future that, if it happens again, it is caused by corruption of the virtual folders. Thanks for your help.