What must one do, who took money from a charity and spent it, and then repented, but is currently unable to return it, for his repentance to be sound?

What you did is considered a betrayal and an unlawful appropriation of people's money. You must return this money to the institution whenever you are able, and it remains a debt upon you until it is returned. It is not necessary to inform the institution that you stole it; rather, the objective is to return it in any way that does not harm you. If it is impossible to return it to the institution because it has ceased to exist or its rightful beneficiaries are unknown, then you must spend it on the general welfare of Muslims, such as the poor and the needy.