I'll agree with the others Randy, Dan, Dave, etc. - former FDIC, lending compliance since 1986, Fair Lending by a baptism of fire 2 years later, etc. You can add to an application, but when you take someone off, it is a different request for credit, because as stated above, someone is preventing the loan from approval.
If your boss wants another opinion, there are many good COMPLIANCE attorneys that will provide one. BOL is trying to help cut down on $500/hr attorney fees. (For gosh sakes, don't refer her to a RE closing attorney an ambulance chaser - not when the fines and penalties can run into 6-7 figures.)
Exams from a fair lending standpoint - if they are looking at comparable files and select your one in question (and notice it), it could trigger a larger search. Sometimes, they regulators the creditor document the exceptions, with regulator oversight, each file found being an ECOA violation. Oh, they will go back to the last exam they tested, so it may be a while. Also, the 25 month clock will come to a stop - telling the creditor not to destroy any files.
Integrity. With it, nothing else matters. Without it, nothing else matters.