DAMMIT! I just S ranked the first chapter again and still got an A. I could have sworn I did every single fight but apparently I missed the fifth one. Ugh, I really didn't want to have to use walkthroughs, but I guess I have to. Maybe chopping of that one guards arm in order to get into that gate skips a battle? Rofl, TIME TO DO IT AGAIN!!!
Yeah, just use a walkthrough at this point. You aren't on the first playthrough anymore, so there are no spoilers, and it's not really cheating or anything. Most of the missable fights involve backtracking at very specific points (which are often not in any way hinted), or not using stealth at certain points. If you are going for the S Rank, there is really no shame in knowing where the fights are. And besides that, it's helpful to know which fights are not ranked, so you don't spend 20 minutes restarting a fight repeatedly only to find out it didn't even count.
Also, I think I know the fight you are missing. Right when you get to the point when you need to get the guard's arm to open that gate, before you open the gate backtrack to where you fought the helicopters. There will be another fight there. If my count (and my memory) is correct, that should be the fifth fight.
Edit: Beaten