Is it permissible to reclaim money from an entity later found to be engaged in unlawful (haram) activities, with the intention of giving it away in charity, or must it be left?

There is no issue with the permissibility of recovering the principal, even if you knew that investing in that entity was forbidden, because Allah Almighty says: "And if you repent, you may have your principal sums; you do not wrong, and you are not wronged." As for the profits, the ruling differs concerning the permissibility of taking them when one was unaware of the prohibition.