The data that was used to build the map is gone permanently.
It also scrambles up the map script so that it's very difficult for a human to read. These are things like: trigger editor data, preplaced unit data, level info, etc. To keep this at a very basic level, protection removes those world editor only files. It also adds certain 'world editor only' files that are used in opening up the map in the World Editor, but not used in actually playing the map. For example, the scripts file (war3map.j), the units file (war3map.w3u), etc. When you launch the World Editor and save your map, the World Editor generates an MPQ Archive for you and then adds the files that WC3 needs to have in order to play the map.
An MPQ is a type of file that Blizzard invented, and it's basically a file that contains other files - imagine a.
Regardless of the extension, though, these files are referred to as an 'MPQ'. I thought I'd write this up to help people understand how pointless it is in most cases. It seems there's a lot of misconceptions about what deprotection can do for you and when to request it.
