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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
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