I have exactly the same problem. It only appears with icloud account not with gmail.

Since then and after several reboot of the iMAC, it seems the problem is gone. No idea why and how. However be aware there is an issue with iCloud, see "iCloud login problem on Sierra, High Sierra", see: https://discussions.apple.com/thread/253811711. So it might be the cause... check if you are on Sierra or High Sierra. That discussion solved my problems with iCloud

Just restarted Thunderbird, as there was an update. Again the folders of the Apple email were mostly gone. E.g. the folder "Sent" came up for a second and disappeared. I performed "Subscribe" and got the folders back I need. So, there is still an issue why the folders disappear and one need to force them back.

Ok, it seems I found a solution.

I found something here: http://forums.mozillazine.org/viewtopic.php?p=2117012&sid=71e0883eda3066a74200784baab69801#p2117012

Basically for whatever reason most of the time when restarting Thunderbird (91.8.1 on Mac) practically all folders have been gone or invisible - on the IMAP server they are still present. Apple Mail works just fine, the problem never occures here, but as a decade long user of TB that's no desktop option for me. It seems that the folder subscription information gets lost or is never properly saved in TB for iCloud. But there is a setting in TB where it no longer relies on subscription but always show all folders anyway - see the link above. To get it properly working I did the following: 1. for one last time subscribe ALL folders first and press OK. Then wait at least 5 minutes since TB updates this in the background! 2. Quit TB, restart, then wait until ALL msgs have been reloaded, this might take a looong while 3. Then do the setting as described in the link above - uncheck "show only subscribed folders" That should be it.

Background: This problem only occured with Apple mail. I used to have every mail on Gmail - a huge IMAP structure built over time. I now decided to completely switch to Apple iCloud Mail. I already had an iCloud account in TB before what with little mails and few folder - never had a problem in Thunderbird. Then I copied all the GMAIL IMAP folder to the iCloud account - that took really looong, but it worked. But then after restarting TB the next day, the problem with the lost folders happened... That's the story.

deleted - double post