Do you put the unique troll's on the discard pile when defeated or do you put them "out of play" because they where not in the deck to begin with?

That question can be asked in general I guess: Do unique encounter cards go out of play when defeated?

I don't have the cards on hand to check, but I don't hink the unique trolls have victory points so they should go in the discard pile. You' also have to check the rules slip that came with that set just in case it says there.

As for other unique cards, they go to the discard pile unless they have victory points and you defeat or explore them.

They go in the discard pile.

Yup what raidskull has said - Discard pile. Only cards with Victory points stay out of the re-shuffle zone!