Gene is correct.
If, however, your e-mail service provider does not have good spam filtering, simply responding to the pop-ups, which used to allow you to mark things "not spam" when they weren't, teaches Thunderbird, and pretty quickly they stop.
As Gene's instructions note, this is an adaptive spam filter, which means that user input about what is spam versus not spam gets integrated into its filtering decisions. But you have to train it.
I've only ever seen this happen on new installs of Thunderbird or where a 3rd party uninstaller was used that obliterated all previous traces of Thunderbird and it has to start from scratch. There's also the option to uninstall and reinstall, as there could have been some corruption that's occurred somehow. (Or, if you're still on Version 68, doing the manual upgrade to 78).
Brian - Windows 10 Pro, 64-Bit, Version 2004, Build 19041
Always remember that computers are just glorified light bulbs - they rarely fail in continuous use and usually go pop when turned off and on.
~ Technician with the username Computer Bloke, on Technibble.com