Is it permissible to waive one's dues and [work] permits to the manager in exchange for receiving money he has hidden and returning with a new visa or transferring sponsorship to avoid final expulsion?

Your sponsor has no right to compel you to relinquish your entitlements or possessions. If he unjustly forces you, you may take your right from what he has with you without his knowledge (the issue of "al-Dhafar" - taking one's right by force when unable to obtain it otherwise). However, it is not permissible for you to voluntarily relinquish your right and then take something from his property without his knowledge in exchange for what you relinquished.