Any patent granted on actions THAT ARE PERFORMED BY SOFTWARE is an invalid patent. Because software is maths, maths is unpatentable, and any patent that says "you can't run that software" is an unlawful patent.
Patents get granted all the time. The USPTO doesn't bother reviewing them for validity. Damages get awarded for invalid patents. If you want a classic case of some poor defendant getting screwed for millions over invalid patents, look at the Blackberry case! (Though if you actually read what happened, rather than get taken in by the propaganda, RIM screwed themselves.)
You are correct to say that if a device using Code A infringes a patent, then another device using Code C to do the same thing will also infringe. But that is a clear statement that the patent protects an idea, which is NOT ALLOWED by patent law! In other words, any such patent *must* *be* illegal! Patent law is only permitted to protect "reductions to practice". So any patent that covers Code A can't also cover Code C because it is a different reduction to practice!
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