the error message show that the directory is not empty, perhaps you can backup the app, delete web2py and recreate web2py (start from scratch) then restore the app
e.g. backup application in pythonanywhere console
mkdir -p ~/appdata/webapp
rsync -zhavur ~/web2py/applications/* ~/appdata/webapp/
delete web2py from pythonanywhere, then recreate web2py
e.g. copy back from backup (step above)
rsync -zhavur ~/appdata/webapp/* ~/web2py/applications/
best regards,
stifan