Hi
This is bit of a mess.
First ensure if the returns are not filed whether payment have been offset. If yes then interest and penalty will not be applicable but late fees of returns will be applicable which will still be huge.
But if liabilities have not been offset then mere deposit of money in portal do not amount to payment of tax. Interest and penalties will be applicable and late fees too.
I suggest you to change your consultant and engage a different consultant with proper remuneration.