Help With PKHaX Save File Corruption

[XOY]

Hi everyone,

I'm currently playing a randomized and modified version of Pokémon Sun using the Lime3DS emulator, and I ran into an issue I hope someone can help me with.

I'm still early in the game (just after the second Kahuna), and I wanted to enable Mega Evolutions using PKHaX. However, when I edited my save file to unlock Mega Evolutions—or even when I just tested a small change like adding 1000 Pokédollars—my game shows a “save file is corrupted” error when I try to load it.

What’s strange is that this doesn’t only happen with Pokémon Sun. I’ve also encountered the same issue with Pokémon Black 2. I’m doing a randomized Nuzlocke with some friends, and when I tried editing my save file the same way they did, my game still gave me the corrupted file error—while theirs worked perfectly fine. I eventually had to ask one of them to make the changes for me, even though I followed the exact same steps.

Has anyone else experienced this? Is there something I'm missing in the editing process? Could it be a compatibility issue with Lime3DS, or something related to how I'm exporting the save?

Thanks in advance

[XOY]

Hi again!

Sorry to bump the thread, but I’ve seen that @theSLAYER has helped a lot of people with similar issues in the past.
If you don’t mind, would you be able to take a look at my case too? I’d really appreciate any advice or insight you might have!

Thanks a lot

Edited July 20, 2025 by XOY

[theSLAYER]

5 hours ago, XOY said:

Could it be a compatibility issue with Lime3DS, or something related to how I'm exporting the save?

Could be, but I don't use that emulator, won't know for sure.

What you could do is export the save file, and see if PKHeX can read it. (Note, PKHeX isn't meant to work with ROM hacks, but if all you've done is randomization, then it should work)

[XOY]

Sorry for the late reply, and thank you for your help

Just to clarify—I'm using PKHaX, which does work with randomized ROMs (my friends use it the same way without issues). I’ve tested opening the modified main file in PKHaX, and it works fine—the changes are saved and visible when reopening the file

The problem is that even though I follow the exact same process as my friends, my emulator (Lime3DS, the same they use too) gives me a “saved data game is corrupted” or “save file not found” error when loading the edited save. Meanwhile, it works for them

Could this still be an emulator or export issue? The last thing I thought of is whether my antivirus could somehow be interfering, but I’m not sure if that would really make sense

Edited July 21, 2025 by XOY

[Kaphotics]

Restore your save file correctly. Do not put unrelated files in the save data folder the game loads, otherwise it will indicate the container is corrupt. 

Try restoring the save file to your 3DS; this is user error.

[XOY]

Well, it turns out that just now—after reading your comment and thinking about it a bit—I tried something new:
Instead of naming the edited file "main modified" (or something similar), I simply named it "main", like the original one.

I had saved the original file in a separate folder, and then replaced it by deleting it from the data folder and leaving only the new file named main in its place.

Just doing that fixed everything! The game no longer shows the corrupted file error, and the changes are applied

What’s strange is that my friends didn’t have to do it this way, and I’d seen some tutorials where people do rename the file to things like “main modified,” so I didn’t think it would be an issue... but hey, as long as it works, I’m happy!

Thanks so much to everyone for the help!