Hello.
Yes, all other users that try this have experienced the issue. They are the ones that brought it to my attention.
When I just open the PDF from the SP library in the browser, it opens as a PDF normally would when you open it from SP. That looks normal. It looks like I'm unable to generate the new PDF from the Excel file in Office online because I don't have that option when I try to save a copy.
I re-read your previous response and think that I may have misunderstood your suggestion. When I am working in the .xlsx file from the Excel desktop app and hit Save As > PDF, normally I just save in the location that's already set, which is directly in the SP library. I tried to instead hit Browse, manually browse to the sync'd document library in OneDrive and saved it there. Only one copy of the PDF file was saved and it was in the SP document library, not the personal downloads folder, which is what we want.
So when you manually save it that way, it appears to work. Unfortunately I feel that this is just a workaround and my users aren't going to understand why this is happening or accept that they have to save that way each time. Is this by design? Is there any way to get this to work correctly?
Thanks for your help.