It doesn't effect your result because in CBSE
There will be no mentioning of the percentage
Only the six subject along with marks are mentioned on the mark sheet.
But some colleges only need your PCM marks only.
Hope you get my point what I want to explain.
Any query
Welcome.

Hello Nilesh, 

Well i think it is not possible. Marks of any of the subject cannot be replaced with another subject marks. 

One thing can happen that is one subject with less marks will not be considered. But this totally depends on the college and there admission criteria and there admission process. 

All the best.