Hello,
If your rank is 11k in jee mains it will remain 11k irrespective of how many students go for IITs.Not all who have better rank in Jee main get that better in Jee advanced.
And moreover some prefer top NITs than lower branches in IITs.
Seperate ranks for jee mains and jee advanced result are declared and then it is upto the students whether they want to go for IITs or NITs.And as their is reservation for some categories,that too have a case .

Hope that helps;

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