How to set my iPhone was always seen in iTunes via wi-fi?
I used to run into this problem all the time, and it was very frustrating.  The only thing that made any difference was to edit the settings of my wifi router to assign both my computer and the iPhone permanent, static IP addresses on my home network.  My iPad still occasionally disappears from iTunes, but this has cut down the frequency of the problem by about 85%.

I assume that this happens because iTunes caches the mobile devices location on the network, but doesn't update it very frequently.  Then if the device shows up with a new IP, it chokes.