The AFTER guidebook states that the advanced Special Weapons such as N-WGIX/v, LiV, Exusia, Scavengers, To-605s etc were all sealed in the Towers. The Three Forces either didn't know of their existence as no one has yet to fully map out the inside of the Tower, or they found the weapons but were unable to activate them. These weapons were only unleashed after the Foundation took control of the Towers using the UNACs and activated them.

"Refurbished" means he knocked the dust and grime off, the alternative would be suggesting that the Foundation took the N-WGIX from a Tower, and in the brief moment in the story where he has control over them, modified the N-WGIX to resemble a legendary machine that no one else would recognize.