What is the ruling on receiving fees for software that is suitable for Islamic and commercial banks and others, and requires modification to the purchasing entity's software to function, knowing that the company is contracted with Islamic and usurious entities and others, and that its current work includes Islamic and commercial banks?

If you know or strongly believe that a program will be used for something unlawful (haram), then it is not permissible for you to sell it, modify it, or maintain it. As for your work in a company that provides services to both usurious (riba-based) and Islamic banks, it is permissible, as long as your work is not exclusively specialized for a specific unlawful entity. If you are asked to create a program that will be sold to all banks, then the sin of selling it to usurious entities falls upon the seller, and your salary is permissible for you. Dealing with a company whose wealth is mixed, partly lawful (halal) and partly unlawful (haram), is permissible, though refraining from it is better.