Hi Mhenry982,
Thanks for the clarification, it seems that there is something wrong with your OneDrive application, because, if we choose to “stop sync” (not “pause”)a synced SharePoint folder, actually, it will unlink your device.
If we need to re-sync the SharePoint folder, we should go to the browser and link it manually, however, you said that your SharePoint folder will re-sync automatically after rebooting the device, I speculate that the operation of “stop sync” is not actually completed.
In this case, you can try to reset your OneDrive application and check whether it will re-sync automatically.
Best Regards,
Arck