Even if an FIR is submitted, you can't get absolved from the compliances under the above-mentioned act. Therefore, please also try to retrieve the register with the help of the Leave register. This is possible only if you have posted the attendance every month after the wages/salary has been paid.
Just imagine how you would proceed in PF and ESIC where individual contribution has a role to play. How will you fill in 3A of the individual employee? The paid challans will only give you a consolidated figure. The leave register will help you at least arrive at the wages/salary of employees for a 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, a small difference here and there won't matter. For this, you can convince the Enforcement Officers.