I have no idea what caused it. This happened during my backup process so I lost about a month worth of personal emails. Definitely a nuisance but i don't think I lost anything critical.

It looks like the offline backup process needs to be:

- Download emails with thunderbird (using IMAP so they aren't deleted online)

- Then backup the local emails

- Then finally delete them from the online folder

Or keep continuous, incremental backups of your local disk. IMO that's a good idea regardless to avoid losing stuff.

Personally I prefer to leave everything on gmail as well as the local backup though, so it's all searchable there.