I am running into the same issue. I checked my save files and there is a futa variable set to true. However I tried to set mine back to false and it didn't seem to do anything.I went along with Amy and her issue to play the game and 'help her feel better', but now she wants to keep the dick. How do I get her to lose it completely? I've pretty much lost interest in this VN since she decided to keep it and it's way too much effort to start again. She is the only one in the game I have entertained this with, and now that I have no choice, I feel the whole thing is waste of time and should be on the ignore list.
I would suggest to the author that maybe needs to ask that question from the start of the game so you can make the choice, or else make it very obvious when that choice occurs so there is no mistake. I liked the game enough, but started to notice that nearly every character started sprouting into futa 'all the time' and I've seen enough now.