THE THIRD ROUTE
There are two routes. Side A (normal) Side B (weird/snowgrave)
But what if there was a third route?
It would explain why there are 3 save files.
In chapter 3, the ERAM and Shadow Mantle games are called the Sword Route in the files.
In later chapters, you can see a crafting recipe for the Twisted Sword, requiring the ThornRing and the PureCrystal (which i reckon is all of the 5 crystals fused together)
You cannot get all 5 shadow crystals if you do the weird route, making the PureCrystal impossible, and you cannot get the ThornRing in the normal route without doing and aborting SideB( the weird route), making the ThornRing impossible, which means the Twisted Sword is also impossible on SideA or SideB
This means that the third route is the Sword Route, making you have to get the ThornRing and abort the weird route to get all of the shadow crystals.
The Twisted Sword is the key to the third route. The Sword Route.