i guess, possibly
*.py are ever running in “python interpreter”
so you can not delete them.
in JAVA mode the
delete source directory
idea works.
if you are able to delete single files ( but not the .py )
to cripple the project so it is not so easy to recreate,
i don’t know.
but as i think open source ( and even open hardware ) is the right way
i am not very motivated to help you.