When setting the shader, the customRenderQueue is resetted in the material. So when the user set it back to the previous shader, the visual is different because the customRenderQueue is resetted to use the default one.
What is happening here is the intended behavior according to the [documentation |http://example.com]:
"Note that if a shader on the material is changed, the render queue resets to that of the shader itself."
The recommendation here would be to let the user know that he should also set the customRenderPass when setting the shader if he doesn't want to use the default shader one.