Is the remaining amount in my possession from the old company's papers permissible for me as part of my unpaid due, or must I return it to the company owner?

If you are certain that you have money with the aforementioned company owner, and they are unjustly withholding it from you, then it is permissible for you to take it by stratagem, provided you do not exceed the amount that is rightfully yours. This is the preponderant opinion among scholars.