DevWareX will warn you when your FPGA and/or FW needs to be upgraded, and will let you launch the "HardwareUpdate Tool".
Here's a link to its User Guide.

In the rare case where the Stage-2 FW doesn't work and the Demo3 becomes unusable, use the following procedure to be able to overwrite the FW.

1. Unplug the Demo3.
2. Find MIS0 and GND, and jumper them together.
   This will ground-out the Flash-based storage device, making it look “Empty” to Hardware Update Tool.
   
3. Plug-in the Demo3.

4. Run Hardware Update Tool; select “Next” and you should see “unknown” for the “Current Firmware”.
   
   If you don’t, you didn’t correctly perform Step 2.

5. Remove the jumper from Step 2, and then continue with the normal upgrade of “Current Firmware”.