Does anyone remember "Luxury Ball" from a gen 4 set. can't remember which, but it basically said "search your deck for any Pokemon card, and put that card in your hand. If there is a luxury ball card in your discard pile, this card does nothing". the card was placed as a single copy in every deck at the time.
Where i'm getting at with this is, there will probably be a Rotom dex trainer card that says "If your GX Attack counter is faced down, put it face up again. If there is a rotom (WHATEVER) Dex, in your discard pile, this card does nothing."
^this is the most probable prediction to how the TCG will handle this mechanic.