For people having people with PkHex. I recommend outright deleting the backup, seriously. I tried editing both files so everything would be the same and it just didn't workout, some changes I made stick, but others didn't, so I tried deleting the backup and ever since then everything has been working smoothly. So yeah, get rid of the backup and work only with the main.
Thank you! I managed to get it to work by just constantly saving both, switching between them and saving again, it's effortful but at least it works. If I have a problem again I'll definitely try deleting the backup. Thanks again!