It's too late - the "damage" is already done. Besides, it's been discussed in another thread that bad Indigo Brotherhood faction will not keep you from doing business in Neriak. Stay away from the warrior guild house. No big whoop.
FWIW, I am working on Cabilis faction and while I am dubious or better with many groups therein, the bankers still scowl, ready to attack. But they don't attack, and I can use the bank as normal. In contrast, I still haven't been able to sell my junk to a dubious merchant in Cabilis.
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