Yes, you will get commissions if the user has clicked on your Flipkart affiliate link and purchases any product.
But the purchase should happen in 24 hours of time after clicking on your affiliate link.
Please refer - https://affiliate.flipkart.com/faqs
The session begins when the customer clicks through a Special Link on your site to the Flipkart Site and ends upon the first to occur of the following events:24 hours elapse from the customer 's initial click-throughThe customer places an order for a productThe customer follows a third party link to the Flipkart Site that is formatted with an Associates tagWe will only pay referral fees on eligible products after order, payment, and shipping.
Cookie will be inactive if any orders are placed by the customer or within 24 hours(until any order gets placed).
If the customer is going to place an other order, again after clicking on your Flipkart affiliate link, you will be eligible for Flipkart affiliate commissions for the second purchase too.
Whenever, an order is placed the cookie gets deactivated.
Hope you got a clearer picture.
Flipkart Affiliate Team