FYI
I have preferences in the IDE that I never change
I also have the serial monitor at the right instead of at the bottom.
This morning I found the serial monitor at the bottom and the two mentioned settings were changed to their defaults. The setting.json did reflect that as did the timestamp of setting.json.
Windows 11
IDE 2.3.6
Your settings likely reset because the IDE rewrote a fresh file. This happens when settings.json gets corrupted, locked, or blocked. Crashes can trigger this too. OneDrive or antivirus can also interfere. Make a backup of your settings. You can mark the file read-only. Check Windows Defender for blocked access. Avoid syncing AppData. Reinstall the IDE if it keeps happening.
I agree.
Question why that would happen?
I did consider that. I don't use OneDrive (although the directory is still there) and I did consider Avast; not sure why it would lock a file for reading.
I actually would expect the IDE to tell me if it could not read the or write the file; I did check the IDE logs in C:\Users\bugge\AppData\Roaming\Arduino IDE and there is no mention of settings.json.
Did that already 
But thanks.
Often, over the past fortnight, IDE pop-ups have asked, "Settings changed, reboot?" in the middle of a session, which I refuse/close. Perhaps germane?
I was also thinking there might be a relation to Title bar unexpectedly switches to "custom" style · Issue #2440 · arduino/arduino-ide · GitHub.
For the sake of searchability, I'll specify the verbatim text of the dialog:
A setting has changed that requires a restart to take effect.
Press the restart button to restart Arduino IDE and enable the setting.
There might be a relation to that; however there was no message like that. I did get that message a couple of days before I reported the "new" issue here but it did not change the position of the serial monitor and I did not have the problem with the disappearing title bar / menu bar; it might have effected the other settings without me noticing it.