I could find a way to make the pokeballs work but it would be incredibly complex
You can either molecularly destabilize it, disassemble it's cells and compress them, or squeeze them into a tiny space if they're small enough (with injury unfortunately)
last option wouldnt work bc when in a pokemon hp doesnt change unless your at a pokemon center
some pokemon dont really have cells so this also wouldnt work
molecular destabilization is the only feasable option
Dynamax pokeballs would probably expand, and for a pokemon to dynamax, it's cells would probably divide insanely quick, but that would only allow for a quintuple in size max.
a lot of cells would have to die rapidly too for when the effect ends
maybe its some kind of fast acting cancer that takes over the body for a short period and then dies out extremly fast
Believe it or not I can actually create a scientifically plausible version of pokemon; I surprisingly wouldn't have to change much but I'd still need to change a lot