@leafgreen357
To fix your issue, download a new ROM. The LeafGreen ROM that comes with the RG35XX is broken and causes the SS Anne issue. I think it’s against the rules for me to link the ROM here, but you can easily find it on Google; just look up “Pokemon leaf green ROM” and the first result should be the one you want.
So first, download that new ROM. Then load that ROM into the emulator (use the mGBA core if you can) and create a new save by completing the beginning sequence then performing an in-game save.
Next, take your original .sav where you’re running into the SS Anne glitch, and use the tool I mentioned above to convert your .sav to .srm: https://thysbelon.github.io/gbaconv-web/
After this, you should be able to open the .srm file in PkHeX. Or I think you can also just manually change the .srm extension to .sav but I haven’t tried this.
If you edit the file in PkHeX, save your changes to a new file, and name the file to exactly match the name of the fresh .sav you created using the new ROM. So if the new ROM’s file name is “Pokemon - Leaf Green Version (U) (V1.1)”, rename your .sav to “Pokemon - Leaf Green Version (U) (V1.1).sav”.
I can’t remember if PkHeX saves as a .sav or .srm (or both?), but if you end up with a .srm and need a .sav (i.e. if you aren’t using RetroArch), just run the .srm back through the tool I linked above and it will spit out a .sav.
Lastly, replace the fresh .sav/.srm with your desired .sav/.srm, and you should be good to go.