It’s normal for CPU usage to pin at 100% the entire time you’re encoding a video file, there's a lot of processing going on.  


Your system will shut down before any damage is done; my laptop shut down last week after I made a video, encoded it and then continued recording another video directly to my HD, but I did save the files.

 

What is the room temperature where the PC sits? 

You must be aware that heat also comes from the power supply, GPU and the RAM

 

Have you tried turning off your PC for an hour before you encode a video file?