Will M. Baker
Yes, they are intended to be "one-shot boosts", and therefore discarded after use. I was one of the editors of the rules, so it's on me that this isn't more clear. I apologize for the confusion.
Think of each cypher as having the following ability:
Village/Dungeon: If this is the first cypher you have used this turn, discard this XP token to [insert cypher ability corresponding to cypher color].