Form16 shows investments as done - But I will go by New Regime

Respected Members,

With my employer, I provided details of investments which have come on Form 16 but I find New Regim beneficial.

So will IT department simply ignore form 16 values under investments (deductions etc) (which won't be anymore there in ITR) when I choose New regim or still raise a query when they do actual processing of filed return?

Thanks