If I could import messages from this profile into a new profile / installation, maybe that might help? How to do that with multiple accounts, mail subfolders etc?
After trying everything I could think of I gave up trying to fix TB 91.
What I did was uninstall TB 91 and install TB 78. Since the profile data was upgraded by 91 I could not directly use the same profile data files. But since I wanted to keep my years of emails, I did the following process to keep Inbox etc files. Hopefully this helps someone else in the future.
Run TB 78 after install, creating a new profile and profile folder. DO NOT SELECT TB 91 PROFILE FOLDER when creating profile, you want to make an entirely new profile folder.
Setup the account settings (advanced/manual setup) for receiving (POP or IMAP) and SMTP for sending BUT DO NOT CHECK MAIL (leave password blank to ensure TB can't check mail). This sets up the account settings.
Exit Thunderbird
Now what I did was copy the mail folder contents from the 91 profile's account to the newly created (and mostly empty) mail folder for the profile I just created.
In the 91 profile there is a folder \Mail containing a folder for each account. I had to figure out which folder was used for the same account that I just created and copy it to the \Mail\xxxxx account folder for the profile that I just setup. If you have a bunch of accounts for that profile then you will have multiple folders under \Mail folder. What makes it worse is that TB seems to name these folders based on the POP server name, so if you have multiple accounts that connect to the same POP server then you will have folders named something like pop.yourdomain.com, pop.yourdomain-1.com, pop.yourdomain-2.com etc.
One way to try to figure out which account is in which folder is to open *.mdf files with Notepad or a text editor and examine contents (such as the "To:"). The other way is to just copy the contents of the folder (i.e. the contents of pop.yourdomain.com folder under \Mail) to the newly created profile's \Mail\<account> folder, overwriting any files. YOU MUST EXIT THUNDERBIRD BEFORE YOU DO THIS.
Then open TB and check the account's Inbox folder to see if the files you copied match up with the correct account. That is, if you setup nuclear_response_team@yourdomain.com the inbox contents should be for that account and not sleazy_politician_slush_fund@yourdomain.com because this could cause unintended embarrassment.
If incorrect, exit TB and delete files inside the newly created profile's \Mail\<account> folder.
If you have multiple accounts within the profile you will have to repeat the process for each account.
The only disadvantage is that address book is not preserved but I can live with that. I believe the address book format has changed between older and newer TB versions.
There may be a backup program or better way to do this but this is how I did it manually.