First of all don't be confused, choose what you want to do in future and if you like to do MBBS then go for it don't look back for nit and all.

But if you don't want to go this way then you can apply for counselling in JOSSA and submit the fee in the allotted college and when the neet counselling starts then go and sit in that counselling too and if you get good college for MBBS then go for it. And just forget the first installment that you have paid in nit because there is no to get that back again, as per rules of JOSSA.