Checkpoint/Pkhex won’t restore edited sav?

[GoldenArbok]

Update 2: This seems to be a SoulSilver, PKHex error/glitch. (Not 100% sure, feel free to test out and let me know.) 

I’ve tested this out on 2 original SoulSilver cartridges, and I’ve had 2 different PC box problems. 

The 1st SoulSilver: I can edit and save everything on the SoulSilver file, except Pokémon in the PC, it won’t save the PC box edits from the SD card. 

Example: I’ll back up my game with checkpoint> pop the SD card it into my pc and open the file in PKHex>
I’ll give myself 100,000₽, 1 Master ball, and edit my level 10 Ekans to level 11, and give it +6HP, +252ATT, and +252SPD EV’s. > I’ll save the edits to the SD card> pop the SD card back into the 3DS and restore the newly edited Sav> I’ll turn the game on and I’ll have the 100,000₽, and the 1 Master ball, but the Ekans is at level  10. It doesn’t save Pokémon or edited in the PC. 

The second SoulSilver: It will edit the box is like normal, but I’m getting the blue screen “save file could not be loaded,  will load previous save” about 10% of the time, when I start my game after an edit. 

Note, I’m not doing any crazy edits to these Pokémon, just leveling them up by 1, and Maxing out EV’s. 

I’ve been using PK hacks for a few years but this is the first real error/problem I’ve ever gotten. If you know what’s going on please let me know.  

 

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update 1: Still don’t know what’s going on but I have learned, I can edit my Pokémon X, Pokémon platinum, and another SoulSilver game just fine. It seems to be this specific soul silver game cartridge I can’t edit. Anyone know what I should do?

I can’t figure out if it’s checkpoint or PKHeX. Everything is up to date, Luma, checkpoint, and PKHeX. I’m not new to PKHEX, but this has got me stumped. 
 

I can backup my SoulSilver sav, edit it, and save it to the SD card just fine, the problem is every time I try to restore my Edited Sav from the SD card, it will say it was successful restored, but when I boot up the game, it’s the original sav. 

One thing I did notice was the sav type may have changed? Not sure if that has anything to do with it? It is the only thing I can save as though. 

Anyone have any idea what’s going on? 
 

Edited May 3, 2020 by GoldenArbok
Update