TDS applicability

One of client is having one employee who is paid salary as well as commission on sales seperately.

The client is showing both the expenses in seperate heads as Salary and commission (Rs. 3.60 Lacs and4 Lacs approx.)

On commission income my client deducted TDS @ 10% and paid to govt.

However in case of TDS on salary the employee of my client is willing to offer his commission income (after deducting his expenses) in the column Any other income reported by the employee and request not to deduct TDS as total tax deducted on gross amount of commission is sufficient to take care of total income of that employee.

Now my question is - can we accept the claim of expenses made by that employee for which no source of confirmation is available with us and not to deduct the tax. Or do we suppose to deduct the tax as per salary calculations and tell that employee to claim refund in his return of income.

Please guide.