You are destroying data. I don't have time to respond today -- someone will fill in and explain what you are doing wrong.
What you want to do is select the Images to move, export them as a Library, and then import that Library into your "new" Library.
You could also simply put your entire current collection in a Folder in Aperture, and then move things, _within the same Library_, to a new set of Projects, Folders, and Albums that your create. When you're done, delete the remaining "old" folder.
Dragging to the desktop gets your Aperture Preview. This is very likely lower quality than your original and definitely missing a lot of metadata.
Deleting from the library is destroying your orginal.
So, yes you've destroyed the integrity and file size of your original, as you have destroyed the original.
Gather all the photos you want to move to a project in Aperture.
Export that project as a Library (it's under the file -> export command)
Then import that Library to the other one.
But why bother? Aperture can hold 1,000,000 images in any one library. Why not just use one and the Aperture tools to classify them?