It would be amazing if it was possible to edit an existing PDF. Right not, Goodnotes can't, and the only way to actually have the modified PDF as output, is to manually export all of it.
Imagine you have a sync folder (maybe with Dropbox, or Syncthings, etc), and you open a PDF (that is inside that sync folder) with Goodnotes. You start to edit the PDF with Goodnotes and everybody that has that sync folder, have the edits updated almost in real time. This is not possible right now, while it is possible in other PDF apps like PDF Expert etc..