You might want to get some hygrozyme or hydrozyme. They're enzyme products that help combat root rot. Use it in conjunction with hydrogen peroxide. May not completely cure the rot problem, but it'll go a long way towards keeping them alive till harvest.
Fred
It is my understanding that hydrogen peroxide will oxidize the enzymes, being organic, if used together. I use both but separately as a rule. I alternate application of each every res change and even in hot temps
have no problems. Personally I like h2o2 because it's cheap and effective although not as targeted to breaking down dead matter as opposed to everything organic. I do like the concentrated shit as it does wonders for sterilizing all kinds of equipment. That and rubbing alcohol... or everclear.
To the OP, lesson learned I suppose. As everyone said, you wouldn't have this problem had you worked to avoid this. The good news however, is that it's most likely going to be just fine. I would suggest you remove as much as you possibly can. In doing this you don't want to destroy your living roots but I'm always surprised at how much abuse a well developed root mass can take without much noticeable effect. In your case I would most likely be quite careful but I would tell you I have been rough with roots before and in healthy plants they tend to recover. Some careful use of scissors can help in removing what you are sure isn't still alive. This could probably solve your whole problem if you have the patience and care. Otherwise with application of h2o2 or an enzyme product the dead matter should works it's way out of your root mass and into your reservoir which can then be dumped with regular changes. That is provided you don't have a system that is going to be clogged by dead plant matter running to waste. Good luck either way.