I had the same issue with my 3GS when I upgraded to 4.something...it was so distressing because I have hundreds of apps on my 32GB...I get them mostly when free and then slowly go thru them but I had to redo all of my folders...
but my situation was much worse...I specifically did a back up of the iPhone before the update...and then there was NO back up there...so I was screwed big time...
I lost all of my pics that were not transferred so you know I was beyond mad...because I had also used the wallpaper making apps that use neon etc to make cool backgrounds and I lost all of those as well...
and redoing the damn folders for all those apps is a nightmare...still have not finished it...and 4.something came out how long ago...lol
so I have not updated my iPad for fear I will throw it across the room
too afraid
how about the bug that on the iPhone if you have too many apps to update in App Store that when you update all it removes the apps from their folders and sometimes just removes all the folders all together...yuck that has been a pain in the past
PS I wish you had your comments on the same page as the original article...blogs like that are so much easier to comment on...just my humble opinion