So, how to "fix" it?
To start, I rearranged the 0x1000-sized blocks in sequential order (based on their offset 0x0FF4 value); since blocks 5+ are for box data storage, I can "copy" block 7 and re-label it as block 8; sure the data might be corrupt, but it's better than an entirely missing block. Probably wasn't anything lost, because now that the save file opens in PKHeX (and emulators/cart) it seems you didn't store anything besides boxes 1/2 and 14.
POKEMON SAPP_AXPE-0.sav