Unfortunately, Appraisers and underwriters rule the real estate world lately. I recently refinanced a property in which my my market analysis showed a value of $215,000. To my surprise the appraiser appraised it at $237,000. The underwriter didn't like that appraisal and order a second one. The second appraisal came back at $174,000. How can two appraisers be $63,000 apart!?!?!
Good luck, pleading your case with the underwriters, as they will have the final say.
I had this happen on a home I had listed. Fortunately it was only for a refinance but still the homeowners got a smaller loan because of it. It was lake front property yet the appraiser gave no consideration to that fact whatsoever, he didn't know the difference between a raised ranch and a bi-level and cut the square footage in half, refusing to count the first floor entirely. He even labeled a photo of the toilet "Living room". Everyone who saw the appraisal said this was gross incompetence, yet when it was brought to the appraiser's attention he only made very minor changes (the photo, for example, was never fixed, and the lake front feature was never accounted for) and the bank also refused to do anything. My clients reported it to the State and now, nearly two years later, they are still waiting for the State to respond to their complaint.
It's very frustrating and it is happening all too frequently these days. In general, appraisers are getting paid less, which means more and more incompetence as the good ones get out of the business, and more and more down right incompetence. I wish I could give you more hope, but that just seems to be the way it is these days.