I have six email accounts in Thunderbird. Until this latest version update, they all ran flawlessly. I’m kind of OCD about creating sub-folders to organize my incoming mail into, and so I also have many sub-folders in some of these accounts. Again, never had a problem until the new beta.
Five of the accounts seem to have no problem, but in the account segment that’s last in the list, the first time I opened it after the install, ALL of my sub-folders were gone. Every single one of them.
This particular account is used mostly for innocuous subscriptions that I don’t care that much about, and since I know this a beta version and my other, more important business accounts seemed to be unaffected, I didn’t worry too much about them.
However, when I tried to recreate a folder using the same name, when I clicked Create Folder it just went into limbo somewhere. There is no Archive folder in this account; never was. Next I created a folder with the same name but added a 2 at the end. This also has the advantage of, if the old folders ever reappear, I’ll know which is older.
That worked until I shut down for the night. When I rebooted the computer and my most-used apps the same day, whoosh - gone again. I created three new folders with names further different than the originals. These folders have remained stable for three days - but every day I cross my fingers as I open the account, because I fully expect them to disappear again.
The first time I re-made the folders, I didn’t move email into them, so I thought that might be the case - that empty folders would be “cleared” from the list to reduce clutter. But the next two times I moved email into each folder - I only have three there now as I’ve canceled most of my subscriptions to that mailbox, to reduce clutter. 
So that’s not the reason.
I have no idea why the current folders have apparently stabilized. It also didn’t seem to matter whether the folders were top level - same level as Inbox - or sub-folders inside the Inbox - they disappeared either way.
I’m not sure this is an actual bug, since it only happened in one email account - if you think it is, I’ll make a bug report.
Oh, one thing just occurred to me. This is my @icloud.com email account, which is my Apple ID, and Apple has a 2-layer password system. When I changed my password to my Apple ID outside of Thunderbird, the email password in Thunderbird ceased to work. As I said, this account is of low-level interest to me, and I just let it go for about a month, so I didn’t use the account in Thunderbird for all that time. Do you think the idle account issue could have contributed to the disappearing folders?
Thanks. 