@TusharAbhinav since BitTorrent is peer-to-peer, if both peers waited for each other to send the handshake, they’d just be deadlocked (neither would end up sending it, they’d just wait on each other). You should be able to safely send out your handshake that says that you support magnet links. Any peer that doesn’t support it will just ignore the reserved bits it doesn’t understand.
Could you try sending the handshake right away, and then waiting for the handshake back? I think that should work.