Is it permissible to take an additional 1000 Riyals from the company for the repair of a medical device, knowing that the actual cost of the repair is only 2000 Riyals, this being after the company agreed to pay 3000 Riyals?

You are not permitted to take the extra thousand from the company, because it agreed to disburse it at the engineer's request. As long as he retracted and calculated the repair cost as only two thousand, you are not allowed to take the third thousand for yourself, unless you inform your employer about it. If they give it to you, then there is no harm; otherwise, it is not permissible.