Hi,
make a copy of your project and on the copy try the following:
1: open the scene with your instanced prefab.
2: delete the prefab itself
3: drag the instance ( now howing in red cause it lost it's prefab reference) back into the project assets
Does that help?
Also, try to export your prefab, and work on it in a clean project, and export it back, it may reset things properly. Also try to reimport ALL assets from Unity Assets menu.
bye,
Jean