Thank you to @BLACKBIRD for contributing the Korean Spring League Shiny Poipole. It is added to our github gallery, and @theSLAYER will probably upload it fairly quickly to the site.
@BlackShark this is the reason:
So the save files end up missing a few bytes.
"Standard Fix" will attempt to pad the missing bytes at the end (well, technically it'll replace the whole block if it is too short, in case there are important values/flags in that block, so it can get replaced/be in the correct offset)
Then, if you notice the appearance of red blocks (in your save), that means that the missing byte (caused by the FTP transfer app) is at that slot.
So "Pokemon Box Salvage" mode instead will pad the missing bytes into that Box slot, to attempt to recover the remaining Pokemon.
It's a problem that technically can occur to any device and any generation, caused by FTP settings not being set correctly.
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Frankly, a better way would be for the software to identify which block's checksum is wrong, which would mean that block is likely corrupted,
and iteratively check through every block, but memecrypto implementation is beyond me at this point, so.. user has to check PC for red blocks in PKHeX!