jje,
There’s a middle ground option that you might find useful… storing/updating the PDFs within the project, but opening them via an external editor when you need to be able to do something with them that Scrivener’s internal PDF tool doesn’t support.
“Open in External Editor”, available via top menu, right click on object and button on bottom right corner of editor window. Note that saving changes made to a PDF stored in the project may require that the PDF not be being selected/viewed by Scrivener itself at that time (if is, select something else in the binder to free the PDF up so as to allow the save to occur).
See 14.3 through 14.3.2 in the Scrivener Manual (available in Scrivener via Help > Scrivener Manual, also available as PDF download from the Scrivener web site’s Support page).
14.3 Viewing Media in the Editor
“The editor is capable of viewing most of the file types that you will need to interface with for research and creative use. The footer bar will often change to provide tools for working with different media types. Note that Scrivener is, by and large, not intended to operate as an editor for all types of files. It would take years to design these features, and in most cases your existing applications will do a better job of editing PDFs, movies, and images. Consequently, a convenience button will be provided on the far-right side of the footer bar for most media views. You may also right-click on any media file in the binder and opt to Open > In External Editor, which will open the file using your system default for that type of file, making it simple to load the document in an external editor of your choice. Changes made to the file will be saved within the Scrivener project when you return.”
Also see 14.3.2 Viewing PDFs.
Hope that helps.