You're probably thinking of Final Fantasy 12's Yiazmat. He does, in fact, have 50 x 1 Million HP and a little change.
Final Fantasy games have tried getting over programming limits for a while, as did the Dragon Quests. It started with bosses healing themselves for lots of HP, effectively extending their life total for quite a bit, later getting a little more subtle - Zeromus (FF4's final boss) invisibly restores his health to max upon a phase transition, making the fight far longer than the already substantial 65XXX HP he starts with would.
After him, Exdeath has consists of four parts with 32000ish HP each, again going way over the 65k mark in total, Kefka of course is a super complicated multi-stage affair, and with discs, hardware limitations go away starting from FF7.
I think both approaches have merit, the smaller numbers definitely require some extremely tight design to make it work, which can be both neat to see pulled off and a little stifling, depending on how you look at it. As this game requires actual skill way more than pure numbers, it is way less of a "problem"...depending, of course, on how well you can push buttons with the right timing.