My Yun is also exhibiting this behaviour. After successfully uploading sketches over several days over wifi, the Yun is no longer showing up in the Tools/Port menu. I am able to connect to the Linux side using my web browser and ssh, but the Arduino IDE is now giving the following error, "Board at 10.0.1.3 is not available" when I attempt to upload a sketch. Any help would be most appreciated.
Arduino: 1.5.6-r2 (Mac OS X), Board: "Arduino Yún"
Cheers,
Mike