Definitely be aware of all it does. I'm not saying it's good or bad, just make sure you are informed. Everything really is gone. Depending on how many SP and WL you have, it may not even make a difference...or it may be the solution to all that is wrong with the world. Not having done it myself (nor even thinking I could empty a 250 gig drive to do it actually), I guess I'll never know firsthanded.
If you do the C/D, i'm sure we would all appreciate knowing how many SP/WL you had and what size your NP list was. It would help others who have similar usages.
In my 6 months or so of ownership, except for SP reordering, I have to say nothing takes more than 1 min. usually.