Adruino Yun's Linux environment not working
You might need to re-flash the operating system. Unfortunately it's not a trivial task.

I had to do something similar with a Dragino shield (like a Yun on a shield) that uses the same OS and core chip. Instructions were scarce and hard to follow, plus I run Linux, so there's even less instructions. I worked it out, though, and wrote a tutorial here.

While that is for Linux and the Dragino shield I am sure the basic principles are the same for the Yun - just make sure you get the right image file for your Yun (don't get the Dragino one I link to).

The main thing is to gain access to the boot manager (dr-boot, or whatever the Yun has), which means setting up a wired (ethernet) network and messing with UDP sockets (using nc in Linux - no idea what you can use in Windows).

I'm sure you can find a tutorial for fixing the Yun from Windows (or whatever OS you use) to help you get into the boot manager and upload a new OS image.