Hi Ankit,

First of all try to understand that RD (Route Distinguisher) is the concept of BGP, not individual prefix.

RD helps BGP to make same prefixes identical, When same prefix comes to the BGP it will choose only one path as per the best path algorithm.

What to do if two different customers are using same range prefixes in their enterprise ???

At that time provider creates VRF that separates control plane for each customers & then they apply different RD value to different VRF so that BGP can identify each customer's route individually.

You can't have same RD value for different VRF, make your RD different for each VRF so that it helps BGP to separate all the prefixes and send update to other end.

Hope my answer is satisfactory, Thank you :)