Let's take a senario of a mesh-instance with a material set with:
mesh_instance.set_surface_material(0, m)
where m is a transparent (transparency flag set and albedo color with alpha < 255)
then it is changed to another material with the transparency flag off and alpha = 255
the mesh color changes but is still transparent as if the transparency flag/alpha carry over from the first material.
more over when i change the resource file name for the 2nd material the color remains the same, as if i did not change the filename.
this feels like a project update issue somehow