The filing of returns has nothing to do with the application of the Act. If you are a factory, mine, or plantation, then the women employees should receive maternity benefits. If your business is a shop or commercial establishment employing 10 or more employees, you should provide maternity benefits to the female employees. The only exemption is for women employees covered by ESI, for whom leave and other benefits will be provided by the ESI Corporation.
Filing annual returns under the rules is secondary, and its non-filing constitutes non-compliance. However, it does not affect the eligibility of employees for benefits under the Act.