Copyright doesn't work by "if you could". It works by "if you did". If you took C and modified it to get B, you are bound by C's license regardless of how close B is to A. In theory, if you took a 10,000 line GPL file, deleted all but the first line, and wrote arbitrary code after it, you'd still be bound by the GPL. In your initial example, if you create any chain of patches from C to B, you are bound by C's license regardless of what you do with A. What you do with A is completely and utterly irrelevant to the matter.
Note that if you read source to C, walk into another room and type it from memory, you are still creating a derivative work. A "clean room" implementation rests on the people doing the implementing having no direct knowledge of the original. That is, someone reads C, figures out the interfaces, creates a basic design document describing those interfaces and gives it to someone else to implement.
Of course if it ever gets to trial, it becomes a matter of whether lawyers can prove based on a preponderance of that evidence that this is what you did and in practice the bulk of this evidence will center around whether you had access to the original and how similar your work is to the original. Lawyers are going to lay out your work B and work C in front of either a judge or a jury and say "@tangentstorm had access to C and B is very similar, therefore he likely copied the work and is bound by C's license".
A would enter into it is if you claimed that your B derived from A and that similarity to C is pure coincidence. The more knowledge of C you can be shown to have, and the more similar B is to C, the harder this will be. You can certainly claim that you derived B from A and use patches/etc. as a defense, but if you actually used the process you describe, this would be perjury.
(Also note that this is civil law, where questions are of "preponderance of evidence", not "beyond reasonable doubt" like criminal cases. In other words, 51% likelihood not 99.99% likelihood.)
In the situation like you describe, your best options are either to ignore C completely and derive from A alone or derive from C and abide by the GPL. Trying to "get around" is both unethical and opens you up to legal risk.
NOTE: I should state that I am NOT a lawyer, and if you are planning on anything like the original question, you should see a real one. The general takeaway from this answer should really be that you are metaphorically asking if you've found a good way of poking a stick into a hornets nest.