Yes, it is entirely possible that modding a game could cause a Game Genie code to stop working.
If you are using an emulator, it should be easy to make a simple change in RAM if that's what you need. For instance, if casting a skill causes a number somewhere to count down from 5 to 4, then you just search for all values that change from 5 to 4, and then search again when you change the value from 4 to 3, and so on, and then tell the emulator to hold whatever that value is at a constant. Lots of emulators have functionality like that.