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If you enabled the backup mode at the PKHeX first start, you will just find your unedited save files in the "bak" folder. You can just take Pokémon from the bak files. Drag & Drop the files into PKHeX and you will find your Pokémons.

There are some guides to solve the PID Mismatch. Not sure if they will fix the issue, but it might be a good place to start. Here they are: https://projectpokemon.org/home/tutorials/save-editing/using-pkhex/gen-3-4-only-solving-pid-mismatch-r31/ https://projectpokemon.org/tutorials/save-editing/using-pkhex/pid-mismatch-origin-game-dppt-hgss-r95/

OMG thank you, I found my friends! They're back! Wait, i celebrated too early, all of my friends except for empoleon are fixed. Hes not an egg, but his encounter type PID is messed up. Im gonna try to fix him while waiting for anymore advice/help.

Not even going to look at the saves, cause I got other things to do. But if you really "managed to get it to work for one", then it's rather simple. 1. Get the non-working saves to have the same TID/SID as the working save. 2. Then, clone the Cute Charmer from the working save and use it on the non-working saves.

So back in 2019, I started editing some of my Pokemon across all gens minus gen 5 and 8. After I did that, I found the auto legality plugin online and started using it alongside my tampering. When I started auto legalizing my Pearl Pokemon, it always made it so that they came from eggs, and not their original method of obtainment (Ex: Empoleon coming from an egg, but it was originally from the suitcase). Afterwards, I felt bad for my bois, so I kept trying to fix it, both with and without auto legality, and nothing has worked. I feel stupid for doing it, and I just want them to go back to as close as I can to the originals, whatever IV's they get I don't really care, I just want to fix this.

While it can't help right now, one thing that you can do in the future is use the Save PKM option in the File menu to create a manual backup of the Pokémon you don't want the auto legality plugin to modify, and then try to import them back into your game.