What is the ruling on using personal work equipment after official hours, and how can one atone for this sin and restore the rights to a joint-stock company without anyone knowing, given that all employees do this?

It is not permissible for employees to use the office's photocopiers for personal purposes unless they have permission from the competent authority. Whoever does so must repent and return the value of what they used. If that is not possible, they should give in charity the value of what they benefited from.