It is evidently a fraudulent act by the employer.
Your friend is entitled to gratuity due, regardless of the payment of salary during Covid. This is related to the salary and has nothing to do with gradually. In fact, he is entitled to gratuity even for the Covid period because he worked for the company at that time.
Since the company has already denied to pay the gratuity amount, and I assume they have put it in writing, there is no need to file the form. You and he should directly go to the authority under the Gratuity Act (Labour Commissioner) and file a complaint for not receiving gratuity.