Praise be to Allah.
This mistreatment that has been done to this employee does not make it permissible to you to conceal the loan that he owes, because you have been entrusted with this work of yours, and Allah, may He be exalted, says (interpretation of the meaning): “Verily! Allah commands that you should render back the trusts to those, to whom they are due” [an-Nisa’ 4:58]. The trust and the contract between you and the company do not allow you to deduct the loan. Furthermore, your work as an accountant is a kind of testimony as to whether this loan did or did not take place. Allah, may He be exalted, says (interpretation of the meaning): “O you who believe! Stand out firmly for justice, as witnesses to Allah, even though it be against yourselves, or your parents, or your kin, be he rich or poor, Allah is a Better Protector to both (than you)” [an-Nisa’ 4:135].
Ibn Katheer (may Allah have mercy on him) said:
The words “be he rich or poor, Allah is a Better Protector to both (than you)” mean: do not take special care of him because he is rich or feel sorry for him because he is poor; Allah will protect both of them and indeed He is closer to them than you, and He knows best what is in their best interests.
End quote from Tafseer Ibn Katheer (Dar Tayyibah edn.), 2/433
Do you think that if the wrongdoer regrets this mistreatment in the future, and restores the rights of the one who was wronged, or if the relevant authorities get involved and restore to him his rights, what will be the situation with regard to this loan that was not documented?
What if your action is discovered and they find out what you did? Undoubtedly that will cast aspersions upon all your work.
What you must do is to do whatever you can to support both the wrongdoer and the one who was wronged. In the hadeeth it tells us that the Prophet (blessings and peace of Allah be upon him) said: “Support your brother whether he is a wrongdoer or is wronged.” A man said: O Messenger of Allah, I will support him if he is wronged, but what do you think if he is the wrongdoer? How can I support him?” He said: “Stop him or prevent him from wrongdoing; that is supporting him.”
Narrated by al-Bukhaari, 6952
So show sincerity towards the wrongdoer in order to make him stop his wrongdoing, and support the one who is wronged in ways that will help him to get back his rights without betraying your trust. One of the things you can do to help him is to explain the system to him and tell him how he can get back his rights.
We put a question to Shaykh Saalih al-Fawzaan (may Allah preserve him) about the ruling on an accountant or financial trustee of a company intervening to take money from the owner of the company and give it to someone he thinks has been wronged.
The shaykh replied: It is not permissible for the accountant to take money from the owner of the business and give it to the one who he thinks has been wronged; rather he should offer sincere advice to the wrongdoer and help the one who has been wronged without touching the money with which he has been entrusted. End quote.
And Allah knows best.