Walker wrote that you only have to discard one favor per roll, not per die. So yeah, you do an attack or defense, you add two favor dice to the roll, and you lose three favor points in total - two points spent and one point discarded.
It helps me to think of "favor points" and "favor dice" as two separate things. Because favor points are an abstract resource pool that can increase or decrease as the game progresses from various sources, and favor points are only actually used as dice when you choose to spend them on adding super-dice to a roll, as opposed to spending favor points on activating special abilities like tactics.
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