Sure, there are some, and more which will likely never be found or even known about. Even then, I would wager that most reworks weren't anywhere near as complete as the FFIV or RE2.
One that isn't documented at all is the rework of Holy Striker (Firestriker in the US) for the Super Famicom. There's a flyer out there which corresponds to the original version. They actually reworked almost the entire game, even key aspects of the gameplay and the core level design philosophy, despite being almost completely finished with the original version. You could still tell it was the same game, I guess, but even the little light ball you bounce around was more a weapon to break things and defeat enemies as opposed to a Breakout ball that you had to keep in play with the help of a wizard guardian. I assume the rework occurred because the original iteration was less memorable than the Zelda/Breakout hybrid they settled on.