Is it obligatory to return the excess amounts disbursed to an employee for a period of four years, given that he attempted to stop their disbursement, and is it permissible to consider the amounts he saved for the company as an offset for these excess amounts?

You must continue trying to stop the disbursement of thel allowance and return what you have received from it directly to the company or by any possible means. As for what you have saved for the company, it is its right by virtue of your work, and it is not permissible for you to consider it in exchange for the shift allowance, because the agent acts in the interest of the principal, and any increase gained by the agent reverts to the principal.