It is always better to leave 5 days gap before bill generation if u r opting for NCEMI to avoid this mess. Anyways u can email HDFC and they will ask u to pay the bill excluding that 50k amount. The emi amount will be refunded so it will count as payment towards the bill. Use that email confirmation as proof if any issue arises in future
Another sad part is that this biller is linked to Autopay on BBPS, now they will deduct total bill amount... I need to now figure out how to cancel it for just this one time...