What is required of me after repenting from taking money from agents as compensation for my usurped rights, knowing that I used to think that was permissible for "recovering a right"?

It is not permissible for an employee entrusted with purchasing to take a commission from the seller for himself, because it is a bribe and forbidden gift, and the original right to it belongs to his principal. Therefore, these commissions must be given to your company, and you must refrain from accepting them.

If the company does not give you some of your agreed-upon rights, it is permissible for you to take them from these commissions, provided that your right is unequivocally established, that you do not exceed your right, and that you are safe from being accused of theft. Then, you should return the remainder to the company by any possible means.