I think Ivory's right (although Aalderon is really the one to ask). You're going to have to lower good elf faction to raise Indigo Brotherhood again, then fix good elf faction via quests or the like that do not lower Indigo Brotherhood.
I'm afraid I don't know specifics on who to kill or what quest to do. Wait til tomorrow and I'm sure everyone's favorite bixie-loving bard will swoop in with an answer or two :P
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