So if a card for example that says take a bench Pokémon and shuffle it into your deck and I take charizard do I just shuffle charizard or would I shuffle charizard charmeleon and charmander?
I'm pretty sure they do. When I'm playing ptcgo and the opponent uses a move that shuffles my Pokemon and all cards attached, it shuffles all pre evolutions too.
source: experience
i think the pre evolutions are counted as the Pokemon itself as well, as when I used a scoop up net on an inteleon on ptcg live, it returned the sobble and drizzile to my hand as well (scoop up net returns a non v or gx Pokemon to your hand but discards all attached cards)