What is the ruling on my remaining in my job as a financial manager in a company where a portion of its profits is transferred to another company owned by the general manager through devious means without the knowledge of the other partner, and what is my duty to do regarding that?

As long as you are certain that injustice and unlawful appropriation of one partner's wealth are occurring, it is not permissible for you to remain silent. You did well by advising the general manager. However, since he insisted on his action, you are obligated to change the evil to the best of your ability. This includes informing the wronged partner, provided no harm befalls you, for the Prophet, peace and blessings be upon him, said: "Whoever among you sees an evil, let him change it with his hand; if he cannot, then with his tongue; if he cannot, then with his heart—and that is the weakest of faith." And it has been said: "Whoever remains silent about the truth is a mute devil."