Hello roshan.

From this year ,JEE Main is conducted by NTA and is online.The first phase is in January and second in april.I guess by 2 shift,you mean one in january and one in april.IF so,then yes the student can give one paper in each phase and the better score will be considered.Each student can appear for one paper ,each in January and in April.I hope this cleared your doubt.

Good Luck!