When the immune system is active, you normally give a random card to all your pathogens. When the first deck is finished, you shuffle the two decks together and you create a new deck.
But if there is still one card left from the Deck1 and you have 2 pathogens in game, what do you do?
My guess is that you should randomly choose one of the 2 pathogens and give it the last card of deck 1. Then you shuffle the 2 decks together and give a card to the second pathogens. You resolve the 2 immune cards together.
After resolving the "immune response", you have to trash the card that you gave to the second pathogen. Instead, you need to put back in the shuffled deck the card that you gave to the first pathogen (that was a card of the Deck1). Eventually, you shuffle again the immune deck.
Is it ok? Otherwise, what should you do?