I was having a similar problem where a SharePoint file was asking to grant permissions to a folder that was on SharePoint, but was listed as needing to sync with OneDrive. In the "Grant" window that opened, I was in OneDrive, but there was no option to get to SharePoint. I finally checked to see if my OneDrive was running and syncing in the background. Due to a recent power failure, it wasn't. Once I had that sync back to OD, then I didn't not get asked to grant permission again to the SharePoint folder and I could save and reopen the document like normal.