Is a contractor's depositing of checks into a bank for less than their face value—knowing this and only paying the original amount—considered assisting him in dealing with usury?

There is no blame upon you for completing the transaction. However, you must advise the contractor by explaining the prohibition of usury, and that it is a declaration of war against Allah and a destroyer of wealth, mentioning the verses and hadiths that condemn usury, such as His Almighty saying: "Allah destroys usury and gives increase for charities," and the hadiths cursing the one who consumes usury, the one who feeds it, its scribe, and its witnesses.