Good morning Joseph,
Not a problem we often encounter in Nassau County; more often in New York City. First, there's a reason why the municipality changed the tax rate at some point. Probably there was evidence of more than 2 occupancies in the property and, even though the CofO states 2Fam, the tax clerk decided to tax as a 3.
My best recommendation is to get an Attorney involved to resolve this; preferably someone very familiar with the Town tax code. Your client can attempt this solo, but will probably have a better result with the Attorney.
PowerHouse Solutions, Inc.
185 Great Neck Rd, Suite 240
Great Neck NY 11021
Licensed Mortgage Banker â€“ NYS Dept. of Financial Services