Just like it says, the patch will somehow disabled the cheat engine, so this means simply this:
If u want to play, there are 3 outcome
1.) your flashcart(for example, acekard is able to play the clean rom), so you do not have to patch it and u get to use cheats as well
2.) you managed to find a working patch, but like what has been mentioned, the cheat engine was blocked, so no cheats.
3.) No working fix, so no game, no cheat.
So what this also means is this:
If you want to cheat:
1.) your flashcart (see point 1 above) will allow you to cheat.
2.) If not, you can't, simply that.
And before u typed, how about some sort of AR code to allow you to use cheats, i am sorry to burst your bubble but code makers are not god, in order for u to bypass the piracy measure and use cheats. You will have to wait for your flashcart developed to update its firmware, but if you really can't wait, then just simply go buy the game.