What is the ruling on taking the university bonus after withdrawing from studies and closing the file, then discovering that it has been deposited into the account?

You are not permitted to accept the reward unless the responsible authority at the university grants you permission after being informed of your situation. If permission is granted, then it is permissible for you to benefit from it. Otherwise, you are obliged to return it, because it is a conditional gift that cannot be owned until its condition is fulfilled, and due to the general statement of the Prophet, peace and blessings be upon him: "Muslims are bound by their conditions in what is lawful."