IMAP accounts that can not connect to the server routinely disappear folders other than inbox and a couple of basic standard folders. I would guess you are having connectivity issues, not subscription issues.

Thanks for the reply, Matt. I'm having no trouble receiving mail in the inbox, so it's definitely connecting. When I subscribe all the folders again, then quit TB and restart, I can see all the folders loading. Within a few seconds they all disappear except an odd few that remain. I look at the subscription list and can see the checkmarks for those that remain and the rest of the checkboxes are empty. I've repeated this a number of times in succession and the few additional folders that remain are not always the same.

Let me rephrase the question with information that may make the issue more clear: I have several Gmail email accounts and one iCloud email account in TB, all imap. I'm having no trouble with any of the Gmail accounts and I've had the iCloud account on TB for months. Only in the last few days, TB began dropping all of my iCloud folder subscriptions. I have refreshed (resubscribed) them multiple times and TB refuses to keep the folders subscribed. In one iteration, I had managed to get all the folders to hold long enough to reset filters and rearange some email when (without touching anything) I watched TB drop (sweep away) all of the folders except the expected INBOX, Trash and (interestingly enough) one additional created folder and one of its subfolders. Help!!

What triggers this issue for me is renaming an iCloud email folder in my Saved Folders from Thunderbird. Thunderbird renames the folder, but then in the status bar I'm watching Thunderbird unsubscribe from every other iCloud email folder. I can manually re-subscribe to all of the folders and it will hold... until I try changing the folder structure again in some way by renaming, deleting, etc.