I have go.properties reset to def when I edit the source game-object. Don’t sure if this the same case as yours, but very annoying! Was going to write about it on forum, but saw your post.
So, here I have a Can game object with sprite, collision-object and script on it, and in script there are some custom properties. I have levels as collections with Cans set in different states all over the levels. And when I edit collision-object properties of the Can GO - all custom properties reset to default.
Can this resetting be avoided? Imo it’s a wrong behaviour, but maybe this was done by demand and not by mistake.