There can be complications if you accept a JoSAA seat and then decide to go for Jadavpur University (JU) after getting selected through WBJEE counselling.

Accepting a seat in JoSAA and paying the acceptance fee indicates your commitment to that particular college/institute. JoSAA might impose a seat wastage penalty if you decide to withdraw later. The specific penalty amount can vary. Colleges generally don't seize original documents. They might keep attested copies for verification purposes during the admission process.

https://university.careers360.com/articles/jadavpur-university-syllabus

I hope it helps!