Go to a different ANAC, you can still get your CPL, at least in Rio it is like that.
You can apply for an RNE from abroad, I decided not to because anyway as soon as the PF gives you the protocolo you can work.
The proof of citizenship it's a pretty standard thing in countries like yours with many refugee. In many countries you can hold a passport and not being a citizen, the US, Switzerland,......and Brazil, the one for Brazil even says passport for non-citizen on it, it's bright yellow.
If you get a good lawyer you can get your citizenship in 4 years period from when you applied for the RNE, I will have my citizenship next year.