There is stuff called Restor-it (NOT Restor-a-Finish) which comes in two parts. It is used to treat existing and immediately stop rot in wood. It's even used for historic monuments to treat and patch (separate putty) wood.
It is clear, the consistency of water, mix in two equal parts and apply very liberally. It is also $60 a gallon.
But cutting out ALL rotted areas completely and replacing with new is the thing to do. The last thing you want is to have to get to that floor again. Very important that you cut out the bad.
You could paint restor-it on the old flooring that you are leaving in, that is not rotted. Also treat the edges of newly cut floor. But cut out rotted and replace with new...really important.
Carried at Ace Hardware stores and other dealers on the site.