Tds deposited but return not filled

As an employer, the income tax return for the Q4 of a FY is not filled, now the income tax department has intimated to an employee to deposit the actual tax payable during that particular financial year. While examining the case, i found out that the problem is due to non filling of the IT return for the 4th quarter. Now, my question is, as the TDS are regularly deposited  through bank challan in office TAN, so whether the IT department will be able to find out the exact record of the tax deposited exactly for any employee even if the return for a quarter is not filled. Please comment.