When there are vehicles inside a copy when you paste it back, the chassis is removed from the modules and the modules hang in the air and can't be ent killed or deleted in any way.
They are only gone if using undo functionhttps://prntscr.com/tc65x4
Vehicle chassis removed when pasting
Dont put vehicles there yet or reduce radius with command this should help :)
I'm having the same issue but now cant remove the cockpit from the server just sitting there randomly with nothing around it
Try Object Remover
I tried everything, The cocpit modules are stuck somehow
I even tried to import the copy to Fortify, hoping I could export it back in to the game after removing the objects but they not included in the model when imported to Fortify
Object remover does remove them... example here is how I removed mine once I installed Object remover and gave myself the permissions /object 1module_cockpit_with_engine action remove radius 20 inside false outside true