Wi-Fi sync with iPhone and iPad fails often
I have experienced similar issues from time to time. Normally, if the device is ineligible to sync (for example, if it somehow disconnected from the same wifi that the computer is on), it will disappear from iTunes in the same way if you were to disconnect an iOS 4 device that had been plugged in with USB. I'm guessing the device's connection is somewhat faulty, and is ultimately responsible for it's disappearing (this is just my guess/thought). 

I have found, however, that if I initiate the sync from the iOS device after it has disappeared, that it will typically come back and work well. This can be done from Settings > General > iTunes Wi-fi Sync.