>>54003803This has always been on the lore. When Pokémon vanish after fainting they’re actually shrinking to be microscopic. Apricorn balls and all the pre-modern balls shrunk Pokémon down to hold them. Even the modern Pokémon’s have been shown to store Pokémon in a shrunken state in the manga. The idea that pokemon get digitized is mostly a misinterpretation of the anime lasers and how the PC works.
In fact the shrinking is a explanation for a common gripe on the series. You know how big Pokémon like Groudon or Whailord are so much smaller than they should be when following you in the overworld or in battle? Well that makes a lot more sense when you consider that Pokémon can shrink. They literally just size down for convenience, either as a function of the Pokéball or the Pokémon itself just choosing to be smaller.