Is it permissible for an employee to reclaim a portion of his end-of-service benefits, of which he was deprived by the company's amendment of its law without settling his dues, knowing that he oversees a financial trust (custody) in which the company cannot prove any deficit?

If the company is private, its owners have the right to dispose of it as they wish, and they are not legally obligated to equalize salaries among workers. You do not have the right to reclaim the amount as long as the company has not withheld a right it contracted with you for. You must fulfill the trust regarding the company's funds. If the company is public, and the amendment to the end-of-service law resulted in depriving you of a right, then you have been wronged, and you have the right to claim your due if you can, without causing harm.