Is working on developing a program that allows for data manipulation and changing invoices for the purpose of fraud forbidden (haram)? Or should this project, or only the suspicious parts thereof, be avoided?

If it is highly probable that the project owner will use its requirements for impermissible matters, then it is not permissible to work on it or assist with it, because means take the ruling of their ends, and whatever leads to the unlawful is likewise unlawful. Jurists have explicitly stated the prohibition of selling grapes to someone who will use them to make wine, and renting a house to someone who will use it for unlawful purposes, due to the assistance this entails in committing unlawful acts. Therefore, work only in the permissible areas for this company, and avoid anything that is highly probable to be intended for unlawful purposes.