Should the money be returned to the father's bag without his knowledge, fearing his anger and loss of trust, especially since the questioner will be working with him?

Taking money from your father's bag without his knowledge is a repulsive and reprehensible act. Repentance for it involves returning the money to him. If informing him would lead to his anger, then return the money to him by any means without telling him. You must return whatever you took from your father, whether it be money or other items, unless it was a small amount for sustenance. If the thief repents and returns the money without the owner's knowledge, then his repentance is sound if he is truthful, regrets his action, and resolves not to return to it.