Well, with 27,000 notes in a few hundred folders in Evernote, I would prefer that the export just recreated the folder structure the notes were already in. So, even if what you suggest would probably work, I would never have the patience to do it if I ever wanted to move to another provider - or wanted to keep my files on my own machine.
That's why I find keeping the well structured documents on my machine the only way to work this. If a complete export would place the files according to the folder structure I have in Evernote, it would be a different question. In that case I would not be worried about deleting the files on my computer.