Okay, not only does this not work for me at all, the outcome of backing up and restoring is actually different from when I transferred my data from my original iPad to the replacement iPad.
When I transferred data from iPad1 to iPad1, I lost all my folders (and books and music, since I had already deleted them from my iTunes library), but at least I kept other relevant data, like photos saved on the iPad or DivX movies that were stored as part of CineXPlayer. iTunes also only synced back apps that had a checkmark, i.e. were actually on the iPad.
Now when I restore data from the iPad1 backup to the new iPad2, I am losing not only the folders but also all pictures and CineXPlayer movies. iTunes looks like it is syncing back all apps I ever bought, regardless of whether I had them on the old iPad or not, and -- this baffles me -- some apps that I picked up as "paid" versions during free promo times all of a sudden display ads, i.e. lost their "paid" status (for example USB disk).
This is incredibly annoying. I suspect that it has something to do with the fact that there are new aplications as part of the iPad2 that were not there before (like Facetime) and that that is why iTunes cannot do a 1:1 restore from a backup and gets confused.
Apple dropped the ball on this one.