So does that mean if you wanna back up your save, your specifically get into CFW?
For clarification, attempt to "perform normal play", then go to Settings >System, what does it say on current system version?
Also, you should have the save on your PC for the "file that isn't working".
Please send that our way, unless you are absolutely sure you've already sent it, then that means your PKHeX isn't updated.
You have a few issues on your hand, let's clear them one by one.