Percentile means the percentage of students you have overtaken to grab the present position. The topper of a particular shift of JEE MAIN overtakes  everyone in that shift. So topper's score is considered as 100 percentile.

Rank changes with change in no. of students appearing in exam.

Rank =( 100 - percentile)* total number of student appeared/ 100.

Now, as the number of students appeared in September session is less than the January session, the rank will vary with same percentile. In this context the clear idea is, the students who appeared in September session will be benefited in terms of rank. Because the rank will be better in compare to January session with a same percentile score.