I'm surprised to learn that the backs of the cards are different. How so?
Nations 1 and Nations 2 can absolutely be used together... if the backs are different and you want to distribute them randomly you'll just need to shuffle them under the table, or simply without looking.
They are different on the PDFs in the Print & Play version. It says "Nations of the World 2" and has the flags of the new nations on them, much like Nations 1 has those flags on the back.