Even if FIR is submitted, you cann't get absolved from the compliances under the above mentioned act.
Therefore, please aslo try to retrive the register with the help of Leave register, ( this is possible only if you have posted the attedence every month after the wages/salary has been paid.)
Just imagine how would you proceed in PF AND ESIC where individual contribution has role to play. How you will fill in 3A of the individual employee. The paid challans will only give you consolidated figure. The leave register will help you atleast to arrive at wages/salary of employees for particular month(s). Tally the figure of salary, PF ded.ESI Ded etc with the paid challan, whereby you will arrive at the figure almost nearer to the actual figure. Thereafter small diff. here and there won't mattter. For the you can convince the Enforcement Officers.