An unusual request, but understandable from a pure development perspective
The way I would do this would be to make my backups then experimentally remove the contents of the meshbank, texturebank, entitybank, segments folders. Drastic and destructive, but you would have your blank slate. Off the top of my head, you will need to retain the basic entities and segments needed by default, which you can guess when you start with a blank level map (ie, the grey ground segment, all the marker entities, etc). NOT for the beginner this one. Do so at your own risk!
"We are the knights who say...eki eki eki fatang loopzoing, zanziga....ni"