Is the aforementioned transaction, which involves taking one third of the amount in advance in exchange for completing a software program, permissible in Sharia? And what should be done with the money taken if the transaction is not permissible?

If the design of a program is a known task, but obstacles may arise preventing its completion, an agreement can be made to complete the program through ijara (leasing/hiring) for a known wage. If the work cannot be completed due to circumstances beyond one's control, the worker is entitled to a portion of the wage commensurate with the work performed, as estimated by specialists. If the worker completes the program under a corrupt contract (aqd fasid) that contains gharar (excessive uncertainty/deception), he is entitled to ajr al-mithl (a fair market wage), and any excess must be returned.