What is the ruling on money acquired from investing funds taken from an employer clandestinely, and does returning the stolen money make its profits permissible?

You must promptly repent to Allah Almighty for betraying trust and encroaching upon others' property. Repentance involves abandoning the sin, regretting it, resolving not to return to it, and returning the right to its owner. It is not a condition to inform the owner of the money about the betrayal when returning the right; rather, it suffices to return it to him by any means that does not lead to corruption or embarrassment. As for the money earned from trading with these funds, the preponderant opinion is that you are entitled to half the profit from this trade, and the other half belongs to the owner of the money, because the growth occurred due to the owner's money and your effort; thus, the profit is divided between you.