A rannuncarpus nabbed my filled shulker box and placed it. When I picked up the shulker box, it was empty..
Forge 14.23.0.2512
Botania r1.10-349

This is on a server.

should no longer clear the boxes

Also worth noting that when I tried it, the rannuncarpus placed the shuller box upside down so I couldn't open it

that's because the rannuncarpus just places the default state of everything (it doesn't target any given side of an adjacent block), and I didn't want to change the mechanics too heavily without consideration.