ckEditor Replacing HTML

I had an editor on my page that allows admin to paste in some HTML to edit specific page sections. When I paste it in the source and click save on my code, it saves it to the database fine. However, if I paste it in source view and then change it to the editor view and back, it changes all of the html.

Specifically things that are bootstrap related such as <section> tags etc.

Is there a way to strictly say no matter what it entered into the source, don't change it? Is there any type of bootstrap plugin for the editor so it recognizes these other types of tags?

Thanks