I am not a Labour Law specialist, but I am an HR Generalist. Still, I have some knowledge of what you are saying. We had this problem in our company, but we made a decision in the employees' benefit. We don't deduct any Gratuity from employees' salary. The provision for the same is to be made by the company as a reserve. All the funds that were held were reversed back to employees, and now Gratuity is not a component of employees' payable salary, though it is a cost to the company and maintained as a reserve by the company with LIC.
You are right; we as employees suffer when we don't complete 5 years because the Gratuity is not applicable to us, and we lose the money.
Including Gratuity in CTC
Including Gratuity in CTC (cost to company) is a wrong practice because Gratuity is purely to be paid by the employer to his employee as a Gratitude for the long and meritorious services. If you read the Gratuity act, however, we see that companies include Gratuity as a matter of legal compliance.
Understanding Wages and Salaries
In my view, if you refer to the meaning of terms wages/salaries in the Factories Act, you must be able to fight for your rights. The company has to return the provisions that are deducted from your salary as Gratuity because it is your money, and it was a component of your package.
Since it's a retrenchment, you will additionally get all that is applicable as per rules.
Regards