We've just released a small update on Z5 this morning which may have made your CF positions (net positions) not appear correctly. We'll look into this and make sure that any such glitches are fixed immediately.
Could you please clarify what exactly is your second question? You can most definitely place an AMO for any of your positions, but you would have to select the scrip from the market watch window and place the order. You can place square off orders from your admin positions window only during market hours on ZT or on Zerodha Mobile.
Is Zerodha the only online discount broker in India to give facility to trade all exchanges on 1 NEST platform? Their Zconnect section seems very interesting, planning to open an account any reviews...