As a contractor, when I get a call from somebody wanting some work done, and they mention that insurance is paying for it, I refuse to do the work. If they say that they are paying for it, and they have the money, and whatever they get from their insurance is separate from the job, then I'll take a look at the job.
Insurance companies that I've dealt with, and that I've talked to other contractors about, always try to low ball what they pay after the job is done. I tell homeowners to wait until they get the check from the insurance company before starting repairs. Never trust your agent, or the company they work for. This applies to your wife, son, parent or anybody that works for an insurance company. Do not do anything until you have the money they owe you.
In my experience, the insurance companies don't care about he repairs, or what happens to the house. They will not pay you for that repair again, they never come out to make sure the repairs where made, and odds are good that they wont even answer your calls in the future.
As for the repair, whatever wood is damaged, it has to be removed. You cannot build up on, or next to bad wood. I've done floor repairs on floors with particle board, plywood, and tongue & Groove. A lot of subfloors have two layers of wood. It's a mystery until you start tearing it apart.
I do not believe that you can repair a sub floor from below. The sub floor is designed to be on top of the floor joists. The stiffens up the floor joist, and ties everything together.
I've never dealt the water damaged subfloor from below. I've dealt with lots of water damage from above. It tends to stop at walls and cabinets. I'd be surprised if the floor joists didn't stop the spread of the water damage from below, but I guess it could of still spread pretty far.
I would take everything out down to the joists, then inspect the joist, maybe add another pier or two for more support, spray the joists with swimming pool shok because it's the strongest bleach that you can buy, and then start rebuilding.