It is up to the lender to determine th appropriate amount of insurance. You can use the appraisal, the agent's underwriting value, your own inspections, hazard insurance, etc. to help determine the insurable value, but ultimately, the responsibility rests on the lender.
Every building has some value. Read my post from 2/4/15 above. You might be able to use the demolition cost or functional building cost approach, but you have to have a value for each building located in a SFHA. You should also read the article entitled "Flood Insurance: Insurable Value" found at our website:http://www.bankerscompliance.com/compliance-resources/free-downloads.htm
Concerning the issue of 3 barns vs. 1: Go back to your vendor and tell them what the appraiser reports. Have them do review this property manually (not with automated mapping software) and ask them to send you evidence of their work. They should be able to send you map overlays showing wha they believe is correct. They and the appraiser need to reconcile this issue. They both work for you.