I remember seeing one of those letters back in the early 2000's, they disallowed EIC because they only used the taxpayers Sch C profit and ignored the loss on the spouses Sch C.

I was only a front office person back then, my employer had prepared the return.  I feel like he did send a letter disagreeing with the changed refund, but for some reason it sits in the back of my head that they never did get IRS to agree and the clients missed out on the EIC....I dont think he pursued it too aggressively though, it wasnt a large amount.