The full context -
Let's say you have a CC for which you set an auto debit for its bill payment. Now you can pay the CC bill before the auto debit will hit your account and auto debit will only the remaining bill amount (if any) to settle the bill. Unfortunately this is not the case with loans.
Loans have NACH mandate set which is different from billpay auto debit.
NACH mandate will deduct the set amount from your account no matter what until you cancel the mandate itself. The amount deducted from NACH will be counted as EMI against your loan.
The remaining question then is what will happen if you pay your EMI twice then? The answer is you can't!
This payment option was showing for me when I was lagging on EMI payment i.e. for example, if this month is April then the NACH amount deducted in April was being accounted as EMI amount for the month of April itself. So before the NACH amount was being settled, this payment link went active as HDFC had not got the EMI amount for April month. In one such month when the link was active for my loan, I paid an EMI amount using SBI VDC and got points for it. But after that, I could never pay EMI amount using VDC as NACH was also deducted in that month and then that second deducted amount sat there for next month EMI settlement. When the next month came, Hdfc started adjusting the amount deducted from last month's NACH mandate and this payment link never went active again for me.