Hi jeri holt-minter,
Thanks for sharing the experience with us, we will help you do troubleshooting for the issue.
We noticed you have tried the method via registry, we'd like to confirm if you use the steps below, if not, we suggest you have an try and see if it works:
1.Go to c:\users\your user name, find the duplicate folder you do not want, delete it.
2.Open Registry Editor, go to the path:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Desktop\NameSpace
3.Find registry with the unwanted/duplicate folder name in Data column, delete the registry by right click on it.
Note: please first backup the registry before making any changes. You can right click on it > export to save the registry in another location.
WARNING: Using Registry Editor incorrectly can cause serious problems that may require you to reinstall your operating system. Microsoft cannot guarantee that problems resulting from the incorrect use of Registry Editor can be solved. Use Registry Edit at your own risk.
4.Quick OneDrive sync client, launch it again and set up syncing OneDrive for business files, see if the duplicate folder still appears.
Besides, we suggest you reset OneDrive sync client and see if the issue will disappear.
Press Windows key and R, in the Run window, enter: %localappdata%\Microsoft\OneDrive\onedrive.exe /reset and click OK. Then restart OneDrive sync client and setup syncing OneDrive for business files.
If above doesn't work, please share with us the following information to troubleshoot the issue:
1.Please provide a screenshot about the symptom in File Explorer.
2.What is the version of the user's OneDrive sync client? You can check it via clicking OneDrive icon in task bar>More>Settings>About.
3.You mentioned "once the user rebooted and logged back on the second drive reappeared." does the issue happen when you reboot OneDrive sync client or reboot Windows?
4.In the duplicate folder onedrive1, what content is in it? Is it the same as the OneDrive sync folder?
Best Regards,
Tina