I am not sure exactly what your question is but if you are wondering if there is a risk of a ban then yes.
Anything you do with the console that isn't what Nintendo wants you to do with it can and will result in an eventual ban.
I think that what he's actually askingI think hes trying to ask if there's a risk of being banned if you use a pro controller while running a CFW and then later using it on OFW.