There are too many events, and the boxes are too small to store everything.
Use the Encounter Database or Mystery Gift database to generate things on demand.
Trying to load a file that is originally 19643270 bytes (12BBB86 bytes) is an order of magnitude larger, and is probably a save state, not a save file.
Save properly in game and export the save data correctly. It should match the expected size without needing to force it.
I thought it was just me!! I had this exact same problem in my playthrough despite unlocking the resort as well. And I had at least 7 legendaries, but despite that he was saying the "saving the world twice" quote.