If you kill the crushbone orcs and lose Indigo Brotherhood faction, the only place in the entire game where that matters is inside of the Warrior's Guild in Neriak, and you have to run into the entrance, run down the hallway, and then you'll have problems. That's the only spot.
If for some reason you care about Indigo Brotherhood, you can kill the wood elven scouts and rangers out in Timorous Deep for glorious exp (tim deep has a fine mod) from levels 20 to 24 pretty easy. It wrecks Faydark elven factions of all sorts, but fixes the Brotherhood faction.
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