My guess.
Neo visits it. They make an agreement for Neo to destroy Smith.
Either it gives Neo more powers and info or Neo gives it the source code. (Glowing yellow frames.)
Option 1 - it then explodes (Not shown, but in the commericals)
Option 2 - Neo goes out and fights Smith, comes back and destroys the thing (it then explodes).
No, because Neo isn't the same as before, different human, different mind, different fighting style. Seraph is NOT a previous one, nor is Mero, Archie, or any other male programs in the matrix...Seraph said "You do not truly know someone, until you fight them", meaning that even if he were to ask NEO if he were the ONE, Seraph still wouldn't KNOW if NEO were the ONE, unless he fought him, found out the way he works, how his mind thinks...we KNOW Seraph hasn't fought Niobe or Ghost before, they are human, yet he fights them, truly "knows them". Neo is a human also, and as such, he cannot have fought Seraph before...