I got a reply from another "Agent" at Support this morning. It looks like the 2nd missing card is a non-foil Meloetta from one of the Battle Decks.
Thank you for contacting Pokémon Support! I was able to look into the cards in question and it looks like that second missing card is the non-foil Meloetta (BCR #77) from the Ho-Oh Legendary Battle Deck. I have escalated this issue to the engineering team for further review.
EDIT: I tested this Ho-Oh Legendary Deck, just to see. Sure enough, it shows 60 cards in Deck Manager (in the little window), but if you count them, there are only 59.
When I play-tested the deck, Meloetta DOES show up there. In fact, I used her as my main attacker, but when the game was over, my MVP card was invisible.
When writing them initially, about the new Pikachu promo, I mentioned it might be a 13th "unobtainable" card, and asked if they could reveal the source of this card. They didn't answer that question, but asked about the other 12. It probably won't go anywhere, but it would be great if we resolved these 12 cards that no one can get.
Would you mind replying back to this ticket with the 12 cards that you mentioned were unobtainable for that we can look into this further? We look forward to hearing back from you!
Edited by RobRatt, 13 August 2018 - 08:50 PM.