When our house was built some walls were built on top of the finished wood floors. After Hurricane Sandy, we had a foot of water flood our house. Are we forced to leave the water damaged floors that support the walls? I'm concerned about mold and rotting.
If your wood floors were damaged by flood water and they need to be removed from your house, it may be very difficult to remove the portions of the floor that sit directly under the wall, without also replacing the bottom plate of the wall framing. Of course things get more complicated if the wall in question is a load bearing wall, because then you have to figure out how to temporarily support the load while safely removing and replacing the bottom wall plate.
Keep in mind that if the water damage was bad enough to warrant replacing your home's wood floors, then there may already be mold or other water damage in the wall cavity. If this is the case, then you may have no choice but to undertake the challenges of also replacing some of the walls in your home. If you do this, then at least you will be able to remove all of the old wood flooring and then correctly install the new wall framing on top of the sub floor, rather than on top of the finished flooring.
Of course, the easiest option for you might be to remove only the portions of the wood flooring that are easily accessible and just leave a strip of water-damaged flooring under the existing walls. If that strip of flooring has been completely dried out and treated with a mildew-cide or other preservative, then you may be okay. Obviously, you'll need a local contractor to thoroughly inspect the water damage in your home and help you to determine if leaving some portions of the wood floor in place is even an option.