We know that in Neon Genesis, each Moon was fitted with a Lance of Longinus in order to keep one seed dormant if two moons landed on the same planet, which is exactly what happened to Earth. Adam was put into hibernation, allowing Lilith and her offspring to take Earth for themselves and prosper. If these same rules still apply, seeing as how there are four Adams in New Theatrical, perhaps there are four Spears of Longinus. As for the Spear of Cassius, it may have been kept in Lilith's Moon to hold her dormant.
I do wonder though, if
Shinji only pulled out one Spear at the end of Q, what would've happened? It seems as if both are needed to hold Lilith's remains in place, to pause 4th Impact.