Is it permissible to take the difference in due wages from the employer without his knowledge, and what should one do if it is unlawful and one cannot return the money or inform the employer?

The contract is the law between the contracting parties, as long as it does not violate Sharia. The employer is not bound by anything other than what was agreed upon with the worker. What was stipulated in the contract must be fulfilled. Money taken beyond the wage without the employer's knowledge is not permissible, and it must be returned to him or permission sought from him. If one is unable to do so, it remains a debt owed by him, from which he should pay what he can. In the case of complete inability, sincerity in repentance and the resolve to return it if it becomes possible, along with supplication and seeking forgiveness, suffice.