Is it permissible to sell iPhone games designed with a program that displays a musical advertisement at its beginning, knowing that removing this advertisement requires an annual subscription of $499, and is it permissible to sell these games first, then use the profits to pay for the subscription and remove the advertisement, and donate any surplus amounts?

If the games themselves are permissible, then there is no harm in you selling them. The music in the company's advertisement for the program does not affect your earnings from the games, because it is not intended in the contract, nor is it included in the game, and it is difficult to guard against. It is possible to control it by muting the sound. However, it is preferable to display the games on a program free of music. You are not obliged to give some of your earnings in charity. It is preferable to purchase a program free of music or to delete it if possible without hardship.