modify attached pdfs

If I attach a PDF to a reference, then open it and highlight something, I can no longer save it as the same name by “replace” (whereas I can do that if I open the original PDF and save it). That means that if I save it with a new name, it is no longer attached to the reference and I need to reattach it. Is there any way to change this? It’s driving me crazy. None of my highliighting is staying put.