When playing with Fluid ideology and having already Nature primacy with Tree connection, removing Nature primacy during reform disables the wrong precepts.
Save: https://drive.google.com/file/d/1VTeKLZ1plJ0hq_IQ5X1hGnhU-b8ii3bZ/view?usp=sharing
1) Click Reform...
2) Select Add or remove meme
3) Remove Nature primacy
4) The game disables Rough living and Temperature precepts which are connected to Tree connection, not to Nature primacy
Thanks for the bug report. I was able to confirm this using your save stripped of mods. I'll get a report into the devs for them to address!