I assume it is something on your system, if that was happening to me I would be frothing.

Given the threading is stored in a sessions.json file my guess is you have installed one of those handy dandy security and privacy products that is deleting it. By far the most common to make that mistake of assuming because a file of that name is used in Firefox it does the same in Thunderbird is ccleaner, but I have heard of anti virus packages deleting the sessions file as well. Especially when folk ask for their internet history to be cleared.

Well, I don't have anything but these two extensions running, and my AV is the Windows 10 supplied AV. I would think if that were the cause, there would be a ton of people having the issue. I have no security software that should be deleting anything in the Thunderbird folder. I don't use CCleaner.

Have you tried troubleshoot made (continue in troubleshoot mode when prompted)? It will disable both extensions while it that mode, both have been known in the past to make some strangle things happen on some peoples systems, so it would be well worth looking into.

I can simply disable them, right?

Still have this problem. I did notice one thing, it's only a problem in my inbox! I can move all the stuff from my Inbox with the threading enabled and they appear with threading in the destination folder. However, if I then grab them all and move them back to the inbox, threading is removed!

This is what I'm trying to fix, this is new behavior, threading has stayed on in the Inbox for years before this happened.