Hi Jacob,
For the issue that “I cannot open the file directly in SharePoint Online (I can only work with the file within the browser)”, please first check if your admin has set the settings below for the document library:
Library settings > Information Rights Management > check if the admin has set any IRM policy to “prevent opening document in the browser for this document library”.
Library settings > Advanced settings > Opening Documents in the browser > check if it is set to “Open in the client application”
If you meet any error message when you try to open the file directly in SharePoint Online, please provide us the screenshot. (Please help us remove any private information to protect your privacy)
For the issue that “The SharePoint file mapping is completely messed up within File Explorer”, from your screenshot, I assume you are using OneDrive sync client. Please make sure the local sync folder in your screenshot is the exact one syncing files and follow the steps below:
- Right click the OneDrive sync client icon > Open your company folder, check if this opened sync folder is the same in the screenshot.
- Check if there’re green check icons on the files, or there’re cloud icons on the files. Those icons mean the items are under syncing.
- If everything is correct based on the two steps above, you can try to un-sync then re-sync to refresh the sync process to see the result. Go to OneDrive settings > Account > Stop sync the library.
- If the step 3 still can’t fix the issue, please try reset OneDrive to see the result.
For the duplicate file issue, please refer to this thread, ensure you have checked the “use Office 2016 to sync files that I have open” option under OneDrive settings.
Thanks,
Rena