Anyone who thinks they're going to spend 15 or whatever chapters explicitly searching for Raphtalia just to push her aside because katana hero from space is missing the point of that whole arc entirely.
I also imagine she'll become a story point toward unity between worlds and forcing Naofumi to make a decision based on the previous prophecy / words about choosing the world or its people or whatever it was. If she represents a different world from her own from an heroic weapon perspective she'll likely be tasked with protecting both. And she's his sword, and he's her shield, like c'mon son.