>>11850353I once thought a (I guess good?) explanation.
Basically, while inside the ball, time passes, so the Pokemon isn't converted into information/energy/whatever (This assumption is based on fact that in most games poison hurts pokes while inside the ball) and exists somewhere in physical form. Let's assume there's a space somewhere that the pokes are sent to and from. The actual sending process is a combination of disintegration and creation of matter. The two processes are simultaneous and complementary. The first effect to jumpstart the (let's assume recalling) transfer is creating single antiatoms matching those from the recalled pokemon. The leftover energy from matter-antimatter reaction is siphoned by the pokeball (so you don't create mushroomclouds errytime) and immediately used on creating the same (this time normal) atoms in the aforementioned space. The overall bilance is exactly 0 and is repeated until no atoms are left(since you started with one poke made of matter and ended with one poke made of matter somewhere else). The technological difficulties would be insane to reproduce, let alone maintain 100% efficiency needed, but "lel handwave".
>that feel when your body turns into nothingness. 
