Is the repentance accepted of one who took money without its owners' knowledge, then returned part of it to its owner who forgave him, and gave the rest in charity on behalf of the other owner?

Repentance from theft necessitates returning the rights to their owners or seeking their forgiveness. If it's impossible to reach them, then it is permissible to give the stolen amount as charity on their behalf.

Regarding the owner of the first bookstore, your liability is absolved because he forgave you, provided you did not conceal the amount of money.

As for the owner of the second bookstore, giving charity on his behalf is not sufficient unless it is impossible to deliver the right to him by any means. You must try to contact him and ask for his forgiveness.

If you do not know the exact amount of the right, strive to estimate it and pay what you believe, most likely, will absolve your liability.

If you sold on credit without the permission of the bookstore owner, you are liable for the money and are required to pay it. You can then claim it from the debtor. However, if the bookstore owner forgives you and undertakes to pursue the debtor, your liability is absolved.