I dispute that ANY real estate appraisal is "killing the deal!"
All real estate appraisals are nothing more than one person's opinion of value. Nothing stops any buyer from going to a different lender. No lender is forced to purposely consider one appraisal over another, most especially when it was the lender themselves that altered the scope (the way the appraisal was done), and altering the scope is highly likely to alter the outcome.
Your buyer has lending problems. The entire lending industry has appraisal problems that are of their own making. If the entire lending side had of spent the last decade promoting, demanding, and ensuring high quality appraisals by allowing proper time for them and demanding good appraisers, you would not be going through this. Instead, the entire lending industry has been, and is, actively participating in one giant lie about obtaining quality appraisals and instead only obtain fast and cheap ones without any regard to the skills, abilities, or ethics of who does them.