Income tax retro Indian payroll

Hi Gurus,

IF an EE has tax liability and not declared any HRA (IT0581) from June and and is declaring now in September payroll w.e.f from June then the system is changing the Pay results of June i.e. the system is changing the Income tax amount from previous months this will effect the 24Q and the year end procedures. is there any solution for this?

Regards

Navya