I keep seeing a lot of writers saying 'don't be afraid of the delete button'. While it is true that you shouldn't be afraid to get rid of some of the crap from your novel, you shouldn't delete anything. If you work from one master file then at least cut the bits you don't like into a dump document or something. They might give you inspiration later!
When I finished the first draft of Sanctuary I renamed it to 'Sanctuary Draft 1'. I then opened another instance of it and named it 'Sanctuary Draft 2'. I then went through draft two and edited away, changed and deleted everything I needed to. The raw first draft still sat untouched in my drop box.
I'm now on draft three and that has its own document too, as will further drafts. This means I can go back to earlier drafts, see what's changed, see how I'm improved and maybe even read all those scenes I had to delete. Plus when I'm famous that first draft will be worth loads. (Planningaheadok)