If this employee joined an establishment for the first time after September 2014 with a salary of more than Rs 15,000, he would be out of the purview of the Pension Scheme. Such an employee could either be treated as an excluded employee for EPF as well. However, since EPF is an investment that provides tax benefits along with savings, if the employee and the employer decided that the employee should be given coverage under EPF, he could be registered under the Provident Fund scheme and a Universal Account Number (UAN) generated.
Since he would be covered by EPF but not by the pension scheme, the employer's contribution in respect of him should be contributed exclusively to the Provident Fund without a contribution (8.33% of wages) to the Pension Fund. When he changes employment, the same should be followed. Therefore, there is nothing wrong with this, and you can continue to contribute both the employee's share and your share to EPF alone.