If you aren't using an artificially overpowered character then possibly the "knockout script" isn't triggering properly. Do you have a save point prior to entering the pits? For long modules such as this it is recommended to make periodic save points that you can refer back to.
If you don't have a prior save point that works can you post your .sav (save game) file on a dropbox or somewhere that I can download it? Then I can fix what is happening and post it back to you.