I can see such an appraisal (especially with the IRS involved) being a 4 digit fee. I question whether the IRS has the right to even demand that. Do you have a tax attorney you can get some free or cheap advise from? I wonder if they are questioning, as Glenn said, if this is a real or personal property loss. Not that is still is not deductible, but perhaps in a different way.
The other issue at play is this--did your property as a whole lose value as a result of this flood? In other words, did you have nice lake front property, and now have nothing downed trees and mud? That could be a loss you have not even claimed yet. If it is a possibility--and IF you end up getting that appraisal, I would have the appraiser (who needs to be expert in waterfront property valuation) consider the value of your home BEFORE and AFTER the flood--dock loss, loss of value in use, and view loss, etc. This would be similar to an eminent domain appraisal--like when the government takes a portion of your land for a power line or road expansion.
Not sure who is responsible or who owns the dam in question, there may be more to your loss than the dock.
Maybe some CG on here can comment if they have some expertise in this area...