Then you are making a mistake, and you told me what you did... Hang on... You save the tree in the tileset in Paint and reload in Advance Map, and the tree is unchanged? Try reopening the file in Paint.
... They wouldn't appear in the map itself, as they aren't set to a Tile Space. You need to do that yourself (They should appear in the middle Box thing in Block Editor, at the bottom) (Tutorials are your friend)