Is it permissible for an accountant not to repay an advance he took from the company against his annual entitlements, which he waived in order to obtain a residency permit, knowing that his entitlements are many times more than the amount of the advance?

If the relinquishment of your rights in exchange for obtaining a residency permit was done willingly, and your rights did not exceed the fair wage for the effort and money expended in obtaining it, then it is not considered an injustice. However, if the relinquishment was done under duress or in exchange for something unlawful, then it is an injustice, and your rights remain established. The employer does not have the right to compel workers to waive their rights.