So, Pixelmon 9.0.0+ has a new feature where you can store your Poké Balls in the Shulker and use them in battle right from it.

If you have 2 shulker boxes with, say, 2 master balls in the first one and 3 master balls in the second. If you try to catch a pokemon using these, you will loose two master balls instead of one. So you will have 1 master ball in the first shulker box and 2 master balls in the second.

Greetings,

I can confirm that if you're only using any pokeball inside of a Shulker box, every shulker box on you will lose the same type of pokeball.
Thanks!!