I was having an issue where every change i did got reverted e.g. i would change something in a template scene close the template and when i reopened it every thing came back, I also noted the 2 times this has happened was after adding a AnimationPlayer. After reading this post i started to play around with the player and i noticed that when i turned off the "Reset On Save" (3rd option down for me), my saves where once again sticking hope this helps some one out there
I'm on GoDot v3.4.5.stable.mono.official