Posting both Q & A here as there wasn\'t a post on SO for this kind of error yet, and other links on web-search led to unresolved gihub issues. Here is me just updating a pa
Checking the actual folder highlighted in the error message:
/mnt/STUFF/py36/lib/python3.6/site-packages/~ornado
I found that there was another one of those .fuse-hidden...
files sitting there which is typically while I'm using Geany (text editor) in my folders during its runtime, which then disappear after I've saved by files and I refresh my folder. Somehow such a file got created here as well and never got removed. Note that this might be my OS's fault and not Geany's - IDK. Anyways I removed the file myself and ran the upgrade command and no errors this time.