Yes, the missions stay on the card. You just can't play some of them until you beat the game.
Originally Posted by Queen_Lugia
I don't use "uber" Pokemon , I don't calculate stat values, I don't use cheating devices, I don't breed my way to perfection, and I don't care about natures. I catch my Pokemon the way they are, and treat them like individuals instead of brainless drones. If you use this philosophy, copy & paste this into your signature. (Started by Tyranitar)
(> <) This is Bunny. Copy Bunny into your signature to help him on his way to world domination.