A Microsoft file hosting and synchronization service.
Dear Steve,
From your description, it seems that you have disabled Protected Mode on the PDF files and the issue persists in your environment. If yes, are there some error messages or some icons on the syncing PDF files in your local sync folder? It is appreciated if you can upload some related screenshots.
Note: Remove any private information before uploading the screenshots.
Dop other users in your tenant encounter the same issue? I suggest you also contact the administrator in your tenant to see if he makes the settings to block the sync of the PDF files.
Block syncing of specific file types - SharePoint in Microsoft 365 | Microsoft Learn
Meanwhile, I suggest you follow the steps in Reset OneDrive - Microsoft Support to reset the OneDrive sync client to see the result.
Thanks for your effort and time.
Sincerely
Cliff | Microsoft Community Moderator