I've ran the AFE for the last 15,000 miles as the only mod I have and I've never experienced a problem like you had. I do see a check engine light every once and a while but no loss of power or shutdown. If I was you, I would take my truck to another dealer.
Most will say that. Any intake or exhaust mod and they will try to say that. They say it alters the airflow and affects the regen cycle. Either find a mod friendly dealer or make sure its stock when you take it in.
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