Is it permissible to count large sums of money saved for my employer — which were not part of my core duties and for which I received no wages — as repayment for a debt he owes, due to my inability to return the money I took from him?

As an employee in a contracting company, you are a trusted agent, and your control over the company's funds is a trust. Therefore, any surplus in the company's money belongs to its owners, not to you. Hence, you are not considered the owner until you restore what you took from the company without the owners' permission. We advise you to be determined to return the money to its owners and to strive diligently in doing so.