I apologize if this has been asked before, but when rolling the dice, do Boons (the eagle symbol) take out Chaos Stars? I'm asking this because we have rolled an awful lot of Chaos Stars lately, and I can't seem to find what the rules say about nullifying the Chaos Star.

Nothing nulifies them, but according to the rules a Chaos Star which you can't "use" (for miscasting, on action cards etc...) counts as a bane, and in that way boons will nulify Chaos Stars that can't be used.

That's what I suspected. What I was confused most by was what to do with Chaos Stars that appeared when not using actions, but when using simple skill checks.

Well, according to core rules, you let them count as banes.

You can though extend this by using suggestions, that makes Chaos Stars trigger nasty stuff (dropping your weapon, making noise while climping a wall thus awakening the guards, advance the Villians Plans, etc...).

I also let Chaos Stars (unused ones) count as both Bane and Challenge.