Nyx and Ra were both made from the same Origin. Despite that, Ra had grown stronger throughout the year while Nyx's strength was stuck because of what had happened to him.
Even though Nyx was back to his original strength thanks to Chaos, he still had that same Origin. The same Origin of the two was what helped Ra trap Nyx in the mind maze. Even though he was strong, he didn't want to risk being trapped there again.
The consideration made him decide to fight with Ryder this time. As he hid inside Ryder, even if Ra could put him in a mind maze, Ryder could still use his strength to fight back. That way, he could be at less disadvantage.
At the same time, he wanted Chaos and Ryder to fight together. Just like Ra and Nyx, Ryder and Chaos also shared a fraction of a soul. That could give him strength when fighting together because he knew something that Ryder didn't.