Just because you completed a path does not mean the opponents disappear the next time you enter!! It's been this way for any quest for the entirety of this games existence!
Yeah, I really wish they'd designed the quest so that you could pick up all rewards in one go if you beat the hardest boss. It was such a boring slog to run through the same opponents over and over and over and over and over and over and over again.
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It's been this way for any quest for the entirety of this games existence!