It is true that non payment of wages of an employee whose salary exceeds Rs 24000 will not come under the purview of Payment of Wages Act, but if the person concerned is a workman under ID Act, the appropriate authority can initiate action against the employer under the relevant Act of ID Act.
If the employee is a manager by functions, he will be outside the purview of ID Act and you can fix the service conditions in respect of such employee. Yes, that can include payment of salary in lieu of notice period not served. But if the employee is not a manager, not having any managerial rights and duties, whatever be the salary he is getting, you cannot impose any restrictive clauses like notice or payment in lieu of notice.
If the issue is at managerial level, no problem, you can proceed with recovery.