I had a similar problem. I was debugging a sketch, and every time I uploaded over USB, the device disconnected then re-enumerated as usual, except once after re-enumerating, Windows 7-64 reported "unknown USB device". I was still able to upload over Ethernet, so I didn't worry - it happens occasionally and then clears up. But today, it eventually disappeared from the network, too. I moved it to my laptop (also Win7-64) and no change. The hardware ID in device manager said UNKNOWN rather than the usual USB\VID_2341&PID_8041&REV_0100&MI_00 / USB\VID_2341&PID_8041&MI_00.
I eventually did a hard reset (Hold WiFi reset for 30+ seconds) and it came back to life.
The sketch I was working on used used TIMER1 interrupt and YUNClient - perhaps that had something to do with it.
Kevin