had the same problem. The following was found in another thread on ATV disappearing from iTunes. It was posted by Cima113. I tried it. It brings ATV back in iTunes. Mine has been fine now for a month. I hope this helps someone.
(Copied part starts here)
It appears the best and only known solution for the AppleTV issue (windows) isn’t actually iTunes build 9.1.0.79. After the helpful postings to this thread it appears that the recent update of Bonjour is the actual culprit. Users experiencing this issue (Apple TV stopped appearing in iTunes 9.1.0.79) should try the following if your setup stopped working after iTunes 9.1.0.79.
1) Uninstall Bonjour version 2 :
Start> control panel>> uninstall a program>>> Select Bonjour>>>> Uninstall
2) RESTART your computer!!!
3) Open iTunes…
You should get a message that Bonjour is missing… This is what you want.
*While you have iTunes open make sure “Find AppleTV’s” is selected in iTunes, under:
Edit> Preferences>> Apple TV tab>>> Check box bottom.
(The above step must wait until after you install Bonjour 1.0.6, restart and open iTunes. This option is noy available while Bonjour is not installed)
4) Close iTunes.
5) Install Bonjour 1.0.6 (reputable download site: Cnet’s Download.com see below)
http://download.cnet.com/Bonjour-for-Windows/3000-18507_4-93550.html
6) RESTART your computer!!!!
7) Open iTunes
8) Start AppleTV and …
Go to: Settings> Computers>> locate the “iTunes/Add library” option>>>
Go to PC and Enter code in iTunes.
Restarting after uninstall AND install are critical!!