[HoosierDaddy]

Hmmm, My basement a/c has insulated ducts carrying the conditioned air to the vents. The only air movement within the evaporator chamber is the return air. I don't see how it could rot from the bottom up. I'm thinking there is cabin humidity that collected in that area of the floor so it is rotting from the surface down. You may only have to replace a layer or two of plywood.
Check to see that the ceiling of your evaporator chamber is insulated.