What is the ruling on money taken from LG and a government agency, if it is difficult to return the money to those who were harmed, and is it permissible to donate it as charity?

If you are reasonably certain that what you returned to your father is equal to or greater than what you took from him, then this is sufficient to clear your liability. As for the company, it is sufficient to deliver its dues to it by any indirect means. If you are unable to do so, then spend it on charitable causes. The general manager's pardon is sufficient if he is authorized to grant it. Regarding the department, if it is governmental, it is sufficient to pay the dues to the state treasury if those in charge of it are just; otherwise, spend it on good deeds and public interests.