Check in the RT settings and see if the 'use +/- files' checkbox is checked or not (might say something different - can't remember exactly what it says). If it isn't checked, you are using the new stretching algorithms. If you want to see how much longer it is taking to generate a song, time one with and without the box checked. If you can live with the difference, erase them if you want to gain some hd space. If you don't need the space, leave them there and if you want the speed back check the box. Nothing to loose by leaving them there except the hd space. Your call pretty much.
Good luck.