Reimporting a shader makes all materials in scene forget undeclared properties set from code.

This is kind-of-an-edge case. In the project, I have BuggyShader. It assigns the colour property to the emissive colour, but DOES NOT DECLARE IT in the properties block.

I have a script that assigns the colour on Start.

This works (which might be a bug since the colour is not exposed) - this is the same for any property, not just colour.

However, when I reimport ANY shader, the colour is forgotten (which kind of makes sense since it was never declared, and hence never saved). However, this is problematic, as it leads to very hard-to-find bugs in the shaders: If you forget to declare a material property, everything works as you expect. However, importing any shader suddenly introduces random breakage (I spent the entire day figuring out this was happening).

Ideally, I'd say that either
A) the property assignment should fail (as you haven't declared the property, effective making it one for Shader.SetGlobalXXX rather than Material.SetXXX)
B) If this is too evil for backwards compat, a warning in the editor on setting this property would be really helpful.

2) How can we reproduce it using the example you attached.
Open bugdemo.unity
Hit play
Notice the sphere turns red.
reimpoty "UnusedShader" in the project window.
Notice that the sphere loses it red