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You should go first thing in the morning and see a criminal defense attorney. You should explain the details of the incident and develop a plan for the best way to return this without triggering a criminal prosecution. We all make mistakes... but the key here is to correct your mistake while incurring the least amount of harm possible.
You should remember that anything you say to anyone other than your lawyer could be used against you in court. So don't tell anyone about this... no one.
If you cannot afford a lawyer or cannot get in to see one then try calling your local public defender's office and speaking with one of their attorneys.
The key here is to refrain from giving anyone reason to prosecute you if at all possible. You made a mistake... so you need to fix it. I also think fixing this quickly would be wise.
Please reply if I can help further.
"Exact transactions have never been checked..."
If that is the case maybe returning the entire amount immediately would be better. This way the balance will be corrected tomorrow and the transactions may never be checked. Please understand that I do not know the nature of your business or the nature of the oversight on this account or the nature of your access to it. Nonetheless, a speedy correction can be much easier to explain than one that takes 3 months.
I know you are afraid. Anyone would be... but don't let that stop you from doing the right thing. Return the money. If you get caught then you get caught returning the money to it's rightful owner... personally I would rather be caught returning the money than caught holding it for 3 months. The strategy for its return is a personal decision that you must make yourself... I can only tell you that you should consult a local criminal defense lawyer to help minimize the chances of prosecution and to develop a relationship and plan if an investigation were launched.
It is not time to panic. You know what to do. You just need to do it.