1 - Revised return can be submitted if it is within the time limits.
2 - If intimation is received with a demand for tax from CPC / ITO, you can file application with the Commissioner for revision u/s 264.
3 - If the notice is issued only for hearing u/s 143(3), you can submit your issues with the Income Tax Officer and file revised computation.
If TDS has been deducted but not remitted by the employer, you can take up the issue with the TDS officer also. If you are still continuing in the employment, you may have some problems with your employer if you choose this option. You can only then request your employer to remit the tax and issue Form No. 16, so that you will not have any problems.
Salary is assessed on accrual basis and not on receipt basis. Hence, unpaid salary will also be treated as income only.