For your sanity, I encourage logging into your online account to reassure yourself that all the messages are there. Then, I suggest unsubscribing from Allmail. That folder causes your disk space to be doubled, your send and receive time to double, and your resource usage to be much higher. Allmail is a duplicate of all other folder.

it does not make ANY sense this post. All Mail is NOT an option, neither can you unsubscribe ONLY from this folder. Useless post. BTW I've been using Thunderbird before it was Thunderbird, when it was part of Firefox, and this weird behavior just appeared recently.

I am unsubscribed as are many others, and it is the documented suggestion from Thunderbird. The allmail folder is never needed. Just yesterday, two users thanked me for that suggestion as it improved their system performance. Good luck to you.

I've used the All Mail folder since ever, with not problems... actually I use it a lot to clean emails that take too much space... in one folder I can see all my emails, as I have a complex folder structure (more than 40+ folders)... my mail is sorted automatically by hundreds of filters... it looks like you are a pretty simple user, like most.

I stand by my statement; you do not need Allmail, but it's obvious that you prefer it. I do hope you get your problem resolved. This is the first occurrence I have seen where all messages seemed to disappear.

Is a quick filter set?