What is the method and means of returning the amount taken from the company to its owners, given the difficulty in disclosing this to the company owner due to the circumstances the company has experienced, and in order to avoid accusations of theft or embezzlement?

You must take the initiative to return this money to its owners. It is not a condition to inform them of what happened; rather, you can return it to them through indirect means, such as a message, a postal transfer, or by adding it to their bank account. Sheikh Ibn 'Uthaymeen mentioned that whoever repents from theft must return the stolen item or its value to its owner. He can employ a stratagem by sending it without disclosing his name, along with a message clarifying that the money is from someone who has repented to Allah.