Thanks for sharing the model, @newton.derekt. I can explain the behavior you are seeing, see the screencast below, which also has audio. Basically, you have two very similar bodies on top of each other, the hole is only in one of them, and there are lots of body moves. A few features later, there is a Remove feature, which gets rid of one of the overlapping bodies. This is why the delete appears to get rid of the whole model. The other body is there, it is just located off to the side. So, the delete does only remove the hole, but the side effects make it appear as if the entire body is gone.
As a recommendation, you might have a better experience if you build your components in place, and not rely on Body Move quite as much. It is also worth reviewing R.U.L.E 1, which gives some good advice about working with components effectively.
screencast:
Jeff Strater
Engineering Director