Is the engineer sinful for tampering with employees' attendance and departure times at the manager's request, or does the sin fall solely on the manager, given that the company is aware of the incident?

What the supervisor does by being absent from work and lying about it is forgery and unlawful consumption of wealth. You are a partner in this forbidden act by covering up his absence. The company's knowledge of what you are doing does not make it permissible, as they are partners in sin. It is obligatory for you to immediately cease this action. If you cannot confront your supervisor, then you must inform his superiors or the responsible authorities to protect yourself and ensure your earnings and salary are lawful. Remaining silent about this for the sake of the job is not permissible. If you are fired from your job, know that Allah's provision is immense.