I've been using mobikwik for almost 13-14 months. Never faced issue like your's.
Within 2-3 minutes, it is shown in the current card statement for axis cards.
Your case is rarest, it's likely to be declined and the payment is about to reversed. I suggest you to make a payment without any delay. Additionally, we get a 3 days Grace period after due date during which if payment done, the bank don't report late payment to cibil. Call the customer support regarding this for more clarity. I haven't tried multiple payments but seen so many threads regarding BBPS which restricts multiple payments towards card but you can search for the payment options if you face any problem during payment.
As you said, the card is not showing payment received, you won't face any problem during payment. And if by any chance, both of the payments successful settled, then you can easily get back the extra payment without any hassle. As you know, cibil hit is the main issue here.
Note :- don't rely on either of the (1) 3-days grace period or (2) your last payment.