The 3.6 prefs.json JSON starts with {version:5, while 3.8 starts with {version:7,. When a < 4.0 editor sees a different prefs.json version, it resets prefs.json to the defaults. This is not great, but it is how it has always been for editor versions < 4.0.
What we fixed was so that you can move between 3.8.99 and 4.0+ without losing the 3.8.99 settings. We don't have a fix for moving between 3.8.99 and lower versions. Those lower versions will reset the prefs.json because that's how it was intended to work when they were released. We've improved this for 4.0, but the old versions will still reset 3.8.99 settings.
Ideally you move to newer Spine versions, if not now then eventually. 3.6 and even 3.8.99 are extremely old.
If you can't do that and the prefs.json being reset when moving between 3.8.99 and lower versions really bothers you, then the only option is to write a shell script that copies in a backup of the 3.6 or 3.8.99 settings files and then runs Spine. We can help you write such a script if needed.
