Version 91.1.0, regular mode, regular mode with all extensions off, and troubleshooting mode. MacOS Mojave
I'm seeing something that's probably related. Thunderbird will at times fall out of threaded mode, that is View > Sort By > Threaded checked will change to View > Sort By > Unthreaded checked, and the list of messages won't be threaded. It happens sometimes (but not all the time) when I delete a message (which is moving a message to Trash, so sort of matches the original report), and other times I'll switch to Thunderbird from some other app and it will be unthreaded, so I won't know when it happened. I have enough conversation threads in my Inbox that it's very obvious when it happens, it didn't happen in the previous version I was running (78.13.0), and I immediately started noticing it upon updating to 91.0.0. I don't have a foolproof way to reproduce it, but it happens 3-4 times per day so there's something going on.