Changes made on Pk3ds do not properly load on Citra

[BombermanBart]

Hello. I've made some changes on Pokémon Omega Ruby using Pk3ds. I extracted a trimmed.3ds file and whener I want to test the changes, I rebuilt into a trimmed.3ds and run on Citra.

For some odd reason, only some changes are made, while others not, and this is a recurring problem.

The first time that this happened I edited Maractus, Electivire and Goodra type and stats and Audino + Mega Audino stats. All of them also got ability changes.

I added the Pokémon into my save file using PKHaX (because editing abilities on normal PKHeX won't work).

When I booted up the game on Citra, only Maractus had changes, whilst the others not (I did not Mega Evolved Audino, but it wouldn't matter).

I found a post (https://projectpokemon.org/home/forums/topic/60163-pk3dspackhackv9-not-changing-the-original-rom-help/) that at the end the poster found out that this problem seems a Citra problem. I uninstalled using the software they used and when I installed again, the changes worked perfectly.

The problem is that everytime I try to boot my unmodified Omega Ruby and then boot up the modified one, it seems the problem citated above comes back.

This happnened when I decided to install both versions of Citra to try to isolate and see if the erro still persists or not. I reserved Citra Canary for my modified rom and Citra Nightly for my unmodified rom. When I booted up the modified OR on Canary, now somehow Electivire and Goodra have changed types, but their stats still just like in vanilla.

I'm not even going to enter the topic of before running the modified OR on v1.4 would crash the game, but now it loads with no crashes.

Anyone knows why this happens what could be possible solutions? This glitchy behaviour makes that if I want to modify my OR, I gotta not run the unmodified one, or everything will go crazy Any help would be appreciated.

Thanks

[KAR0TTENP0WER]

do you maybe have stuff inside the mod folder?
Citra -> open mods folder