The headquarters longed for Arya's Blade so they could decode the pattern and principles of its Anti-Magic Glyph to enhance the power of their weaponry.
In the second Otherworld War, one of the most challenging situations faced by the multinational forces in the Otherworld was the inability to penetrate Rune Armor. If they could decipher the Anti-Magic Glyph, they would be able to manufacture Magic-breaking Bullets which could pierce through the knights' armor.
This concept was proposed when the research center was founded. During the selection competition for the advance team, they added this weapon to the computer simulation environment. Clearly, they had figured out that using magic was the best counter to magic.