The note is usually a condition of closing so it is not surprising that they won't negotiate something that they have already negotiated. But that isn't to say that they wouldn't be open to such discussions some time down the road.
Or are you talking about the original 2nd lien note? In that case remember that they may not be in that strong a position. Remind them that you can always go through foreclosure and they get little or nothing.
Dealing with Greentree as 1st lein -- will they allow deficiency waivers?