I swear I read the Exodus rulebook front and back, but I still may have missed this: The rules frequently refer to discarding Trauma Tokens, but it does differentiate that some get added back to the pile of unused ones (Cylons encountering Disaster tokens, for instance). What happens when all Trauma Tokens are discarded? Do you shuffle the discard pile back into the unused one like with Skill Card decks? Or does to "discard" a Trauma Token mean shuffle it back into the unused ones (and this is a terminology problem)?

I've been wondering the same thing. We played a seven player game and said that the tokens would remain in a separate pile unless we could discover something that said otherwise. Even in a seven player game, we didn't make it through the whole pile of trauma tokens. My guess is that is how it is supposed to play, but I guess we won't really know until a new FAQ for this expansion.

True, it may be that they're discarded and never re-used. But usually, that means that they go back to the box and nothing says that

However there is a distinction in the rulebook between "discard" and "return to the pile of unused tokens" So who knows what they meant to say?

Well, i guess by the strict letter of the rules, you make a discard pile and never re-use them. If you need to place or draw new Trauma tokens, you're SOL.

Sorry I don't have a specific reference, but "somewhere" we already had it answer that they are returned to the draw pile. This is especially important for the blood spots! They are "discarded" like a Civilian ship that is escorted off... back to supply. Not "Remove from Game".