I recently bought a second hand copy of Pokemon Omega Ruby that turned out to have this cartridge corruption issue.
I downloaded your tool to see if I can resolve it but it was never able to get past the first chunk. I thought the game was completely gone tbh. When using your tool, the icon for the 3ds files were very corrupt, and when dumped the game icon was just a black square with no text. Opening it would just crash the 3DS.
However, I decided to leave the game on the home screen and on standby. Now the icon for the 3ds files are looking normal, and the game appears on the home screen like normal. Currently it cannot be launched, but I would imagine another week or two on standby may actually fix it.
One thing I also noticed after leaving it on standby is that your tool now hangs after the first refresh. Not exactly sure why, and it never did that before, but now it just hangs. I will have to keep and eye on it to see what is going on with that