Is it possible to expiate the sin of deducting a percentage from the weight of farmers' produce at work, knowing that the company is the beneficiary and not me, and that the manager is truthful in his claim regarding the company's financial situation?

The manager's request to shortchange the scales is Islamically forbidden and considered a major sin. Shortchanging is an usurpation of others' rights, and its perpetrator must offer sincere repentance and return what he has usurped. If the work is conditional upon shortchanging, then it must be immediately abandoned. The manager must also be advised and warned of Allah's punishment. If reporting to official authorities will stop this act, then reporting is obligatory, unless it results in an unbearable harm.