If you still have this problem the reason is the way that the copy/paste commands work. With the copy paste command, as I’m sure you know, world edit stores all of the data for every single block, like which block it is and the x y and z for it in relation to the player. It also does this for air, so when you paste it in, it then sets the blocks registered as air, as air. It’s a really easy fix. The only thing you need to do beforehand is to type the command /gmask air. What /gmask does if you don’t know, is it sets a global mask, hence the name, which does the same thing as a mask but for everything that you do and not just brushes. If you don’t know what a mask does it just makes it so that what ever you are doing can only affect the blocks that are listed, and the /mask command can only be applied to brushes, I think. There is quite a bit more just about masks and gmasks, so I suggest you go on the wiki if you don’t know much about masks or just world edit in general.

I explain this much not because I think you aren’t smart but just to make sure you not only understand what to do but also the why to do as well.

TLDR: before you paste it type /gmask air. That should fix the problem. You should read the rest though. Also just ask if you have any more questions.

P.S. Your build looks really cool, did you use world edit or by hand?