does this plugin remove items in Boxes? When i do the command remove all, every item that was in a box or turret falls to the ground any way to stop that from happening?

your lucky as ive removed many boxes by accident in the past and lost loads of stuff.
Dropping stuff to the ground sounds like a good idea to me.
Also not used /remove on a box lately but it used to not work unless the box was empty

I am a server owner and i copy and paste bases all over my low pop server for people to raid and ones raided i remove them and paste a new one up but sometimes not everything was looted so when i remove all items drop on ground and people are like scavangers trying to get loot that drops

gotya you are removing the foundations so it will fall - that is correct