Ai didn’t know about Aine until the heroine told him. (She had found out prior because of circumstances that led to Ai’s professor telling her, Syo, and Natsuki.)

Prior to the disconnection, Aine’s brain was wired to what I assume Ai’s system (there’s probably a computer or main framework that receives and passes the data between them). Aine can see the data Ai collects but Ai is unaware of it being sent to Aine.

After the disconnection, they’re no longer connected, but Ai’s song reached Aine’s heart and Aine in returned saved Ai from completely shutting down. (In After Secret, Ai said he “heard” Aine’s voice and it led him back.) 

What I theorize is that while they are no longer connected as robot and model, they are connected by the same love they share for music.

It’s no problem! I love talking about Aine.