It doesn't recognize the game in TWL.
I made a new save using his repro rom, and the save was able to be read on pkhex.
OP mentioned the current homebrew 3ds sometimes has issues loading the game, but works perfect on his old 3ds. Maybe could be something to do with this?
He's going to try and homebrew the old 3ds next and retry dumping the save on that device.
Make a backup just incase it happens again. I never seen a glitch like this though, how did you edit the save? You mention you only added 2 pokemons, and items? what items, and what pokemons did you add?
Almost impossible currently unless someone makes a PIDIV calculator, Since the PIDIV's for roaming mons are validated in BDSP . This info is pinned on the Pkhex discord already.
This means making/capturing a legit one, and converting it to shiny will make it illegal.
Try legit shiny hunting it?