All perfect praise be to Allah, The Lord of the Worlds. I testify that there is none worthy of worship except Allah, and that Muhammad is His slave and Messenger.
It is not permissible for you to take money from this engineer after knowing his lies, treachery, and misusing the company’s money. The scholars stated that the one who takes (anything) from the usurper, the thief, or the aggressor is like them as long as he knows that they have encroached on the rights of others. Accordingly, what you took from this forbidden money, you must return it to the owner of the company, even if through indirect ways. Allah's Messenger said: “The hand (which takes) is responsible for what it has taken till it returns it.” [Tirmidhi] Moreover, your silence on what he did is also impermissible, and you could have told the company's manager what he did in a way that did not harm you and prevented his injustice and assault on the company’s money.
Allah knows best.