EZ flash Omega DE - games not saving in mode b after using a slot 1 flash cart homebrew app

[Armando99]

So I had pokemon emerald written to the nor flash and was using it in mode B I used a homebrew app on my slot 1 flash cart on my ds lite to inject event items into the save but now every game I use in mode b will keep reverting back to the original save it was written with and wont save anything new unless I direct boot it in mode A dont know if doing this was safe or if anyone has found a solution for this.