So, either the makers are trying to throw us off by showing Balli's inner monologue or it's actually Balli.
So, it could be possible yeh log dono Balli aur Karan ko zinda dikha dein. No bodies found, toh quite possible.
If it's actually Karan, then I feel Batra Sir ko thodi toh bhanak hai. The way he stopped Faizi from killing him, letting him into the academy so easily, trusting him. Feels like Batra Sir knows it's Karan. Shayad usne explain kara hoga about Param, and they made this plan. The whole don't-tell-anyone, taaki log iss mission ko aur hard naa karein, the whole he'll-stay-as-Karan-Shergill, again for the same reason.
If it's not Karan, then I feel ki shayad Balli is not the one who saved him. Maybe Tilli (or even Param) saved him. Maybe Param bahut years se, as a spy, work kar raha tha (nothing concrete is revealed about him, toh quite possible he was faking that amnesia, kinda thing, or whatever) but since it's his little brother in danger now, he saved him.
Ya Tilli par Karan ki baat ka actually asar ho gaya, and he helped him get out.
Precap mein mujhe laga ki shayad yeh actually Karan ho. The way he dodged that throw (Balli toh seedha zameen par jaakar apna head cover karta, not dodge to the side. Karan usually dodges like that, recalling that first day of training jahan par he dodged the punch from that cadet like that).
Aaj ke baad, ek second ke liye lag raha hai ab, kahin yeh actually Karan Shergill ko mara hua naa dikha dein.