The method you are specifying is for the convenience of the employees.
The method you proposed needs to check as per compliance and operational as below
The compliance issue you are concerned is, lies with the Employer. As per IT dept, the employer has to consider the proofs, compute tax, deduct at source and deposit with IT dept.
In this declaring Investments is responsibility of the employee. To address this, the employer needs to have a Self declaration from employee which usually states the proofs are authentic, complete and further allows employer deduct tax based on the proofs.
Check how you are managing this.
Then you are going to "Verify" and "Update" the Investments. I assume, this is due to if employee uploads incorrect documents erroneously or purposely.
Will there be any alert to employee about updates?
Tax department sends notice to employee if any clarification on tax is required,.
What will be your role in this situation when an employee needs documents of Investments considered in tax computation?