If we're going to "define rape", we must acknowledge that there is a big difference between "legal" and "moral" rape. I e, just because something isn't proveable in court doesn't mean in wasn't rape.
But I think it's an unrealistic idea to try to "define" all rape in way that still respects the circumstances of every case. As a general rule, I feel it within reason has to be the version and feelings of the one who feels raped that matters most. Because even if every logical clue points toward the opposite having happened, if somebody honestly feel that they were being raped, well... They still went through the experience of being raped. If, like in the above scenario from ed boy, there really was no way for the "rapist" to tell, and he really would have stopped if he realised she was no longer consenting, well, that's a shame for everyone involved, but it doesn't really change what she was feeling. His intentions doesn't really change her experience. I can't with good conscience say that her version of the night didn't happen just because the guy didn't realise (and in the given scenario couldn't realise) that sex was no longer wanted. He may not be a rapist by concious choice, and may be horrified by the thought, but I still think you have to say it was a rape. Indeed, I feel a better question for the scenario might instead if "was it rape?" but "is he a rapist in every sense of the word?".
Beyond that. The thing with scenarios like this is that since we weren't there, we can only guess and assume at was what going on. Why did she stop consenting? Why did he not notice?.why didn't she way anything? All circumstances that matters, but we don't and most likely can't know beyond doubt. Since this is a personal story as well, we can't assume you know all the details either, or that you aren't influenced by your trust in the involved people, or even that they told you the truth as they experienced it. All thus reasonable doubt makes individual cases like these really hard to actually comment on without jumping to conclusions... I'm not sure I feel getting involved in arguments over such incidents, when all I know about them is a few paragraphs long text, will lead to any constructive development.