rhizome appears to be talking about people negotiating settlement agreements where the payments are clawed back when a patent is later found invalid. This would take agreement on both sides before the settlement, and I doubt patent holders would go for it. Worth a try though.
In your analogy, the activity was illegal until the law was changed. If a patent is declared invalid, then it shouldn't have been valid when it was used in prosecution, so it's logical for the defendant to ask for some kind of redress. Whether the law actually works like that, I don't know.