I had a look into it a bit more and this are what I find for my project.
Scene change / Save load error-
xyz is right. Those errors are caused by my scene change script. I need to read more into how to update it.
Model mesh and textures not found-
Majority of errors are from this but the solution turns out very simple (apart from project > tool > update mesh). Somehow it requires update the naming of import mesh eg, "playermodel"(4.1) to "player_model"(4.2). That was why the textures and model were missing and probably caused the corruption of my player.tscn. The fix is to get your original .gltf and copy over to your project again and it should update the name for you. (Then you need update your model path in your script too)
Shader missing-
I could still see the shader on the model but not while running the game. Probably same solution with updating the path, but haven't look it so not confirm yet.
I guess I was a bit over reacting (tbf though with all those red errors popping up everywhere 😆). So yea with 4.2 you need to pay attention to your model update and scene change, as document suggests.
@Rogarth
That's why I jumped to work on 4 only and not 3. Though, I anticipate there will be major upgrade later on physics and IK so I don't bother doing anything on that just yet.