They don't need to. Police is actually required to enforce law and can file chargesheet at will ( most of the time), they only need to interpret the law. The police in this case does not needs to take permission, since the courts have not cleared Kanhaiya 'formally'. They have only accepted the forensic finding that the video of slogan was fake and doctored.The charge sheet is clearly on the grounds of "hosting an anti national even in JNU" and there are still a lot of things left to be proven right and wrong.

Law and procedures are a finicky thing in India, with often opposing and conflicting procedures on both sides.

Unfortunately and ironically, till Kanhaiya actually goes to the court as a defendant and the court clears him of all charges, this nonsense will continue. He is marked.

There is a history of BJP trying to go after Kanhaiya since 2016 as a way to get political ammunition.

There was a nice article on this entire mess on caravan quite sometime back.