Following up briefly with notes:
Original file (a fresh file, not the one in the above post): 0x380000 bytes, loads in PKHex but it looks like random garbage data.
When decrypted and immediately re-encrypted, the file is identical to the original file, so I assume there's nothing broken with the save tool.
Upon changing the TID/SID and re-encrypting, only the bytes 0x12860, 0x12865, 0x12686, 0x12687, and a handful in what I assume to be the checksum (0x1BFF87 through 0x1BFFBF) are different. In PKHex, the TID/SID have changed and the rest is identical (that is to say, garbage data.)
After using PKHex to insert a few actual Pokemon in place of some of the garbage in box 1, there is no visible difference in-game. I still can't access custom passes and the records screen show I have zero Pokemon in storage.
Original and edited save files included as attachments.
PbrSaveData-new
PbrSaveData-original
