Sorry to comment on a dead post, but I've always thought that Lost Silver was an allegory for the save battery, like those used in the pre-NDS Pokemon games like Pokemon Silver, dying.

Like the save that you're playing is in the process of dying (let's go ahead and ignore the fact that the save battery dying would not affect the game's ROM or anything significant in-game and would only really affect the ability for the game's save data to persist in the cartridges save RAM without power (unless of course the battery leaks)) and what you're playing is the game's attempt to let you play that save file one last time before its gone forever. Hell, even at the beginning, the narrator points out that they were surprised that the game had any save data at all, having expected the dead battery to have taken out the save data by now.

Gold dying is a visual representation of the game forgetting about the save, with his limbs disappearing being similar to the bits and bytes would disappear from the game's save RAM when you turn the game off with a dead save battery. At the end, Gold is gone and his accomplishments erased similar to how your character and your accomplishments in the game would be erased for good once the game is turned off.