Same thing happened to me with my ipod touch (newest generation). My entire workout history was wiped clean while my total distance ran, calories, time, etc remained there. It's a real shame that this happened after updating to iOS4. Even worse, the Nike+ application does not run as well as before. The time elapsed stays at the same time when i check on my progress, and only updates after a few seconds*.
* For example, when i check to see my progress, the time might read 56 min 23 sec, and stay at that time for about 6 seconds before adjusting to 56 min 29 sec.
The whole program feels a lot slower as well. Going from the main window to selecting a program type, then choosing the music, and finally activating the sensor takes about 5x as long than before i upgraded to iOS4. I only hope Apple and/or Nike can work together to give me back my history of runs on my iPod Touch so that I won't have to go on my macbook pro and log on to the Nike site to keep track of my runs. I just hope someone out there can help.