Is the user already in an edit session in Arcmap before your script starts editing? If so then I would check with tech support and look into [BUG-000089820: The Editor class from ArcPy returns an error message when the 'stopEditing()' command is executed when an existing edit session is open on the same workspace. "RuntimeError: Start edit session."] I had a situation where the user is already in an edit session so I didn't think I had to start editing in python script but the tech support person had me start editing. However when I went to stopEditing it failed with the error you received and they pointed out the bug. In my case I just removed the stopediting from my script and it seems to be functioning.
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