Problem with appraiser using outdated engineering report

we bought a house with slight structural problems in a very good neighborhood. when we put down the offer, we requested a structure engineer’s report from the seller, which showed a few issues. after the closing, we hired a contractor to fix all the problems and had a thorough renovation.
we decided to refinance the house recently. when the appraiser contacted us for scheduling an appointment, he asked us if we had any engineer’s report for him to refer to. we made a fatal mistake by being too honest: we sent him the old report from the seller but at the same time we told him it was out-of-date since we already fixed all the structural problems. the appraisal report came back very bad: the actual appraised value was ok, but the appraiser attached the old engineer’s report in the appraisal report. actually the entire appraisal report only shows the current condition of the house which is excellent. the appraiser did not discuss a single word about the old engineer’s report in the appraisal, which makes the old report completely irrelevant to the appraisal. but the fact that the old report exists made the bank worry and they denied our loan application. we tried to dispute with the help of our mortgage company but failed. it looks like there is nothing we can do at this point, and we lost some money and time from the appraisal. we think it is not fair for us to lose the loan because of the disclosure of an old, irrelevant report by the appraiser. is it appropriate for the appraiser to do so? does anybody know if there are any rules or regulations for appraisers to remind the homeowners of their rights and disclose their information? is there a way that we can still complain or fight against this situation? any input will be appreciated.