Hacking changed SD and microSD cards and lost half my omega ruby save

[FatalX]

so I recently changed SD and microSD cards for more memory, I reinstalled gateway and all my games by copying and pasting the saves in the SD card, they're all working fine except strangely omega ruby which restarts me from my save halfway through the game. I tried even deleting all the saves on the SD card, and the game still starts me from the same spot despite there being no save.. do the Pokemon games function differently through the save files? why is it losing an older save and what could have happened to my most recent file?

 

[VerseHell]

Pokemon X/Y/OR/SA are card2 games, that means they save directly inside the rom.

 

[Quantumcat]

Maybe it didn't save properly last time you played. With Gateway to get the save to save you have to quit the game with the Home button and then tap Close. Although that might not apply to card 2 games like Pokemon. If it wasn't that, I have no idea but will be interested in the answer if someone can figure it out!