Hello Arnav ,

Since you are going to apply for the BITSAT then you will have to show your new marksheet there and they consider marks in all 5 subjects so that they can get an aggregrate of the marks 

You can concern the concerened person there if they can consider your partial improvement exam 

Here I am sharing a link which has all the details regarding the BITSAT contact details 

https://engineering.careers360.com/articles/bitsat

Hope this will help you in a good way and you can ask for further clarification