I am being told that private insurance companies cannot write deductibles below $2,000, which in some cases is above the amount of the structure.
Is anyone else having this issue, if so how are you handling?

You have to have flood insurance. Who your customer decides to buy it from (NFIP or a private policy) is really not your issue. If they can't find a private insurer then they would have to go through NFIP, if the insurable value is more than the NFIP minimum deductible.