Well this appears to have been fixed in 2018 sp4
925552 Assemblies, External References, Save, Close: Rename assembly (Rename component in Feature Manager Tree) for top assembly file will cause all external references out of context
It would appear it wasn't limited to imported files. I am hoping it is fully fixed because if I remember correctly on occasion just simply going into the part and checking or editing a feature would cause the whole lot to die.
I also wonder why it worked fine most of the time and it was just on occasions.