Who is responsible for the loss of merchandise stolen from the store: is it the store owner, who was entrusted with the money, or the owner of the money, who requested its return before the theft?

The hand of the agent in a Mudarabah (profit-sharing partnership) is a hand of trust (amanah), so he does not bear the loss unless there is transgression (ta'addi) or negligence (tafreett). The demand for the capital and the dissolution of the partnership are only necessitated by selling the goods and converting them into cash.

If your partner accepted the termination and you both agreed that he would pay back your capital and bear the responsibility for the goods, then your money is his responsibility (in his ذمة), and he bears the loss from theft or anything else. He must return it immediately.

However, if what happened was merely a promise to liquidate the company without immediate termination, then there is no guarantee on your partner because he is entrusted (mu'taman), and the partnership remains ongoing unless there is negligence or transgression on his part. It is not permissible to accuse the agent of theft without proof.