Hi Curlyhairedmomma,
Thanks for posting in the community. We are happy to help you.
I understand the inconvenience you are experiencing and apologize for it. Per your description, you are using different applications/services on your computer, and OneDrive is blocking synchronization changes to other applications/services. In this case, you want to stop synchronizing a certain subfolder (the Output folder) without moving it to another location and keep synchronizing other subfolders.
If my understanding conflicts with the situation, please point it out and let us know.
If I understand correctly, please allow me to reconfirm the following point first.
Regarding "but you can't exclude anything in Documents", I would like to know if the Documents folder is the local built-in Documents folder backed up by OneDrive. If not, please point it out and let us know. If so, unfortunately, the built-in "Choose folders" feature in OneDrive doesn't support choosing certain subfolders among the three backed up folders (Documents, Desktop, and Pictures). This is a known limitation.
Based on the above, one possible workaround I can offer is to use the Mklink command to build a symbolic link to link a local path to the local OneDrive sync folder. Here are the steps. See if it works for you.
a. First turn off the Backup feature for the Documents folder in the OneDrive client. Then move all relevant files and folders from the OneDrive sync folder to the local Documents folder (from C:\Users\Make sure that all relevant files are folders are stored in the local Documents folder, not OneDrive.
b. Run the Mklink command to build the symbolic link
Run CMD as administrator and run the following command. Also, check the following points before running the command.
mklink /d "C:\Users\
In the following screenshot, I created a symbolic link to link the Pictures folder to my OneDrive sync folder.

1). Make sure that the "aaaa" folder has not been created in this path "C:\Users\You can replace “aaaa” with another folder name.
2). Replace
After that, you should see a new "aaaa" folder in the OneDrive local sync folder, and all files and folders in the local Documents folder appear both in this new folder and the local Documents folder.
For your reference:
Can't synchronize OneDrive files and folders from a local file location other than the default OneDrive path
3. Use the built-in "Choose folder" feature and uncheck the Output folder.
Based on my test, sometimes, files in the symbolic link (the aaaa folder) will stuck on syncing. In this case, you can manually pause syncing and then resume syncing. After that, you can go to OneDrive for Web and verify the results. See if you can see these files/folders in the browser. If you don't see these subfolders in OneDrive for Web, I suggest you reset OneDrive and then check again.
When you have any updates or concerns, please feel free and come back to share them with us. 😊
Sincerely,
George | Microsoft Community Moderator