Actually, FFXIII-2 did something like this in Chapter Two. When you fight that huge-ass biomechanical called Atlas. Halfway through the chapter, you have a choice: either attack it head-on, or instead head deep into the ruins and activate a device that powers it down somewhat. At that point in the game, it's virtually impossible to defeat it head-on, but later on in the game you can go back to these events and redo the battle at full-strength.
While not quite what you were talking about, it's probably the best example of it I can think of.





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