First off find the reason for the rot and fix that. Then find how extensive the rot is is. Yes you may have to remove any current hardwood flooring to determine this but it has to be done.
While the flooring is a part of the structure you can replace smaller sections without compromising the structure. You can only make that judgment once you have define the problem.
WBCCI 12156 AIR 3144 WACHUNG TAC NJ6
2004 Excursion 4x4
1991 34 ft. Excella +220,000 miles, new laminated flooring, new upholstery, new 3200 lbs axles