Will Piplup From Pokemon Mystery Dungeon Explorers of the Sky Disappear?

Answer 1

no pokemon "disappear" from this game permanently. at one point in the game(when you beat dialga) your character(piplup or not) disapear for a while and the game will show your partner telling everyone about the adventures you went on before you "disapeared", but dialga does something that makes you come back.

but if you're talking about the pokemon that join your team that you release, you can not get that specific pokemon back; you'd have to recruit it again.