The sword and it’s spirit have and forever will be one.
OOC: First, I kind of just like drawing the Master Sword over the Goddess Sword. Second, when I played the game, I just assumed that the sword, as it is in the beginning of the game, is just a downgraded version of what it once was. I mainly thought this because 1) Fi’s look never changes and 2) this wouldn’t be the first time the Master Sword’s appearance has backslide due to neglect and/or time. We’ve also seen the Master Sword’s appearance change in game before, for similar three-task/Din-Farore-Nayru reasons.
I could be totally wrong, but I feel like it’s open-ended enough to debate. If there is concrete proof that I’m wrong just make me aware by sending me an ask so I know.
Also, while the manga isn’t canon, it isn’t the first time we’ve heard of a hero before the Link in Skyward Sword. When Zelda presents Link with the sailcoth at the beginning of the game she references this original hero.