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.

I assume you are opening outside of Endnote to do the annotation?  – If the record is still highlighted in Endnote, the PDF is open in that software too (thus read only), and if you click off of its record in endnote to another record, you should be able to save the PDF to its original name.