Thunderbird "unified folders" not working after moving my profile
Solution 1:
In the end, the problem was fixed by deleting panacea.dat from the profile folder and and all .msf files from its subfolders. These are only cache files, and after deleting them Thunderbird will rebuild them automatically (might take some time, especially with IMAP folders as the message header data needs to be downloaded).
This solution even retained the special folder selection I had on my Unified Inbox.
I found the instructions from this article: Phantom folders