Can't run custom ELF with "Run ELF" - game uses MOVIE.ELF then reloads original ELF

[ciox]

Hello everyone, I hope someone can help me with this issue, I want to run a game's ELF with some small changes hexedited in, this works fine initially, I can change a string to see that the custom ELF is running and so on.
But the game is built so that after you press Start, it runs a prerendered cutscene with MOVIE.ELF and then goes back to the original ELF, this flow gets rid of my custom ELF. 

Can I do something about this or am I out of luck? Thanks for any ideas.

[ciox]

I guess another way around this issue would be to just turn my hex changes into pnach file cheats, but I'm not sure how I'd do that either.