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1) What does it mean when a Sisters' chamber has a glowing, pulsing aura around it? It's been around that girl with the blue tattoo on her face the entire game, and occasionally I notice it elsewhere.
It usually means she wants to talk to you.
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2) What does silver do when in your hearts? I've had no events that seemed random.
Use of colour in chambers slowly destroys the whole group of chambers around the sister. Use of Silver lets you deal less damage to the world (isn't it written in the game's journal?). Better to say, if you have 100% "silver" characteristic ('Cold'), then you deal two times less damage. You may make it even smaller using Red for violent acts, Gold for SIsters or Violet for trees. This way you reach the same effect while technically using less colour. For example, if you choose to release Ole, then you can save 65% of her chamber's health by using 100% gold and silver. However, her realm ends up almost dead if you do this without any Gold or Silver.
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4) Attacking with the color highlighted on the outermost remaining ring during the boss fights did more damage, right? Sometimes I couldn't tell if I was imagining it.
Twice as much, to be more exact. We even included this info in the game's manual, given that there is hardly any info about that in the game (which is surprising to me; though, how are we supposed to explain this without NPC's talking explicitly about the interface?).