This question in SUMO describes a similar issue, and the comments from one of our top support contributors describe some of the troubleshooting steps and possible solutions if this is what's happening to you: https://support.mozilla.org/en-US/questions/1390549

@thunderbird not sure if this is exactly the same issue, in my case the entire inbox disappeared following a failure to retrieve new mails - not just individual emails being deleted, (In fact i have never encountered an issue with individual mails being deleted) then it automatically started re-downloading the entire inbox when i restarted the app.

The best thing would be to open a new support issue in SUMO, and use some of the advice in the issue linked above to paste the relevant details in your post explaining the behavior you're experiencing. This way you have an entire community who can help, and the troubleshooting steps and solution are there for anyone else with this issue in the future. Thanks for understanding and we hope this helps!