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Thanks, fixed in latest commit: https://github.com/kwsch/PKHeX/commit/a450b56878394e6cefdbdcd88c891901182c88f3

I DID IT!! I wasn't using a complete version. OperationiDroid only had the classic version apparently. I had to download a Platinum Rom and patch it with Drayano's patch and then change the name of the newly patched ROM to match my save. It was a little tedious but my Pokemon are strong now. Thanks for the help, wouldn't have checked this if you hadn't said this!

That's because base stats are thoroughly dependent on the ROM, and aren't stored in the save. The base stats you may see in PKHeX is purely visual, purely based on the real game's stats. You can just edit the summary stats, and let that be it.

The stats you see in the summary, are based on a calculation on IVs and Base Stats, that should update when leveling up. While PKHeX does recalculate the stats in the summary screen (and it'll use the non-hacked base stats as part of the calculation), your summary stats should have been replaced by the hacked Base Stats of your hacked ROM hack upon level up. If it doesn't, then who knows what the issue is. An alternative, as I said earlier, is to use hax mode of PKHeX to write the wanted stats.

PKHeX isn't meant for ROM hacks. If you want illegal stats, enable HAX mode. Also, if you level up, it should recalculate the stats based on the ROM hack. Lastly, PKHeX doesn't change typings of mons; it is dependent on the ROM you're running.

The saves are encrypted with a key that is found in the ROM header and is unique to your cart. So without the original cartridge or a ROM backup of it it's not possible to decrypt the saves.

Which emulator are you using? Upload your save file, maybe its format isn't too different from a proper save file.