Unable to save changes made to PDF in External Editor

I wanted to highlight a PDF I am using as part of my research for a short story. I figured out how to open the PDF in the external editor to make the changes I want to make. But once I make the changes it won’t let me save any of them. Every time I hit save I get the following message. “The File may be read-only, or another user may have it open. Please save the document with a different name or in a different folder”.

Do I have to close the scrivener project file before making any changes?

You can avoid the error by loading a different document in Scrivener’s editor before saving from the external program, so that the PDF isn’t still loaded in Scrivener. Ideally that wouldn’t be an issue, but we haven’t been able to get around this particular quirk yet.