The same thing happened to me. I have an Eris. I had all my contacts linked, everything arranged the way I liked it. And for fun I was trying a stupid skin/scenes thing. Now, I only have 3 screens (instead of 7) and all of my saved preferences are gone. It seems like Driod is boasting all these Apps on Marketplace... but you can't trust them.
To make it all worse, I just spent 25 minutes on the phone with Verizon and HTC trying to get it back to normal. Verizon transferred me to HTC and then after explaining, being put on hold, explaining again-- HTC told me that I should call Verizon about a factory reset. When I said that Verizon had just transferred me, the guy would just keep repeating the same, "Unfortunately, I can't help you with this there are problems that only Verizon can help you with." If Americans added up all the minutes that they spent on the phone, going through phone trees, waiting on hold, explaining and re-explaining, giving their information again... it would add up to so much time. So much wasted time.