Yep, the second file I downloaded, gets the same md5 and the size is 20907 bytes..
Seems like its the same hex but you could email me yours to be sure? Three's a crowd 
If the md5 is the same I don't need to email it. Use that one.
Use the 20907 byte file with the md5 sum of 374845d004d03c6ca0535bb4b6f19235
I got it working!!
We were trying to use the wrong HEX all the time.
Instead of Arduino-COMBINED-dfu-usbserial-atmega16u2-Uno-Rev3.hex I had to use Arduino-usbserial-atmega16u2-Uno-Rev3.hex from here : https://github.com/arduino/Arduino/blob/master/hardware/arduino/firmwares/arduino-usbserial/Arduino-usbserial-atmega16u2-Uno-Rev3.hex
md5 ba4b38e08f625cacfbeb3fb4a70d5567
The first sign that got my attention was that this HEX was also 12228 bytes like the HID hex file. They appeared to be identical (at least size-wise).
Although the Flip software is a bit odd and doesn't always upload the hex although it seems to succeed (checked what was uploaded by saving the FLASH as a new file) I finally pulled it off.
Windows greeted me with a new device and after installing the UNO drivers I just successfully uploaded the Blink sketch
Amazing how much relief a blinking led can create.
Big thanks to Nick and Coding Badly for your support!
Sorry about pointing you to the wrong file. I'm glad you have it working.
Wow - this thread just saved me! Successfully got my Uno r2 to be a USB MIDI device. Then couldn't get it back to being an Uno again! Basically all the things in the above posts happened to me too!
I don't have much to add apart from the correct .hex file link doesn't work anymore. I managed to get the hex file from here: /arduino-1.0/hardware/arduino/firmwares/arduino-usbserial/Arduino-usbserial-atmega16u2-Uno-Rev3.hex - Quadrotor - Robotics Club.