What must the questioner do to atone for his Egyptian company's assistance in defrauding a French company, and is it sufficient for him to give money in charity, and how should the amount be estimated if it is impossible to reach the owners of the French company?

The company was obligated to be sincere in its work and to complete it in a lawful manner. You did well by advising the official in charge, and this is a form of enjoining what is right and forbidding what is wrong. As long as you have done what you could, no sin will befall you, for Allah Almighty says: {O you who have believed, upon you is [the responsibility for] yourselves. Those who have gone astray will not harm you when you have been guided.} [Al-Ma'idah: 105].

As for your salary, you are not required to give any of it away as charity, because the contract was based on time, and it is the company's duty to pay the full salary as long as you dedicated yourself to work. If the other company has a right, it is the responsibility of your company, not yours.