What should a person do whose lawful and unlawful money have become mixed, and he wishes to repent, and he has a deposit in the bank from money he took unlawfully from a charitable institution for orphans?

"Whoever repents, Allah accepts his repentance." Your friend must return the funds to the charitable organization in whose name they were collected, because the Prophet, peace and blessings be upon him, said: "The hand is responsible for what it takes until it returns it." If those in charge of the organization are negligent with the trust, then he should return the funds to the donors themselves.