PKSM 3DS save editor deleted my pokémon without me trying to

[Patesaus77]

So, i had some Shinies i caught 5 years ago in one of my PKSM boxes and i sent it to my Pokemon Ultra Moon copy (cartridge). I think i didn't save before exiting PKSM and when i checked my game i saw that the Pokemon didn't get transported over and the Pokemon from the PKSM boxes are gone too, what should i do?

FYI i used PKSM on my 3ds and Pokemon Ultra Moon on the same 3ds which is a cartridge and not a digital copy. If there are any files you want to inspects, just let me know and i'll drop the files here asap!