I agree that the rulebook isn't completely clear. "Received Boons normally go to the Boons
discard pile". The fact that "received" is past tense makes me think you're right; they go to the discard pile after you receive them.
On the other hand, playing this way requires a new place for hexes to be, other than the hex pile and the hex discard pile. There has to be some sort of "resolving / set-aside" area. For other cards, when they are revealed, they are not considered to be moved (which is why Wishing Well doesn't need to provide instructions for when your guess is wrong). If you consider the resolving hex to be simply revealed, and not moved, then you could argue that if you receive another hex before you are done; you would receive that same hex again because it is still on top of the hex deck. I'm quite sure this is not correct, which means that there must be a place for hexes to move to.