What is the ruling on completing a Holy Quran program on a free version, by utilizing files that were created on a cracked version?

You have done well by refraining from using the pirated version. There is no harm in benefiting from the work you previously did on it, to complete it with the free version. However, you must estimate the value of the damage and the lost profit incurred by the program owners due to your unauthorized use. This amount should be paid to the owners if possible; otherwise, give it away as charity. Experts can estimate the extent of the damage, or else, exert your own effort and give out what clears your conscience.