Hello there, everyone! tl;dr version at the end of the post, I like writing. =p
I usually get updated on stuff by a friend of mine, but now I came accross a problem and I thought I'd better just create my own account and try to sort it myself.
I've been using PKHeX for simple stuff: the first, transfer back my Y save from the digital download to my physical cartdrige. You see, back in the day I got a download code for Y, and it was when TSV and stuff were going, so I needed a digital copy in order to check my egg data. I "sold" my physical game to a friend, who eventually gave up on the 3DS and I got my game back: I much prefer physical media, so I extracted and sent my save data to the physical game once more (also, updating the trainer name and ID to match my Alpha Sapphire, just to they'd have the same trainer).
Apart from that, I only changed my Vivillon type, reset the legendaries flags (I caught them all first with my ID, just for collection's sake, but if I ever decide on SR for any, they'll be there), and putting my Maison streak back where it was before losing (I have a very lousy luck, like taking a critical + burn from a Flare Blitz when I had Focus Sash, Fissure hitting twice in a row...), and organizing my boxes wallpapers (much more friendly than in-game). Honestly, nothing major.
However, recently I noticed something: I kept some Pokémon with "message" nicknames like a Spoink named "Thank you! =)" and stuff like that, that would stay in Y's Box 31: this woud give me easy access to them during trades. I decided to send them from my digital Y to Pokémo Bank, and then move them to my Sapphire (my current main game). It was then that I noticed, as I moved "back" from Box 1, Bank would show me Box 30. After 30, Box 1 again. I finished the Delta Episode long ago, and I actually have stuff stored in Box 31. However, I only noticed this now, I can't recall if Box 31 was showing before I started "HeX'ing" my save file. I compared to a friend's save, and his save also got "13" for Unlocked BG flags and the "Unlocked" dropbox also is up to 31. I even put my event flags for legendaries the same as his, but Pokémon Bank still refuses to read my Box 31. I changed wallpaper, moved every Pokémon out there, nothing. Any idea if any sort of flag I changed my accident may be "blocking" it?
tl;dr: Pokémon Bank doesn't show my Box 31 despite it being unlocked, nor I'm sure if it was displaying before, I realized this just now. Can this be related to any flag in the save file?
Thanks in advance for any help!