I don't know the ins and outs, but more stuff seems to get deleted (cookies? Or something) if you do it the other way. Mine is definitely going faster since I did it.
Also try 'killing' all your apps. Double click on the round home button and all the apps you've ever used will show up in a row at the bottom of the screen. Hold down for a couple of seconds on one of them until they all start wobbling and have a little red circle with a white line through it. Press the little red circle until all the apps vanish from that row.
It won't delete any of the apps and they all still remember usernames and passwords, etc. I just find that it helps it speed up a bit.