Hmmm, I don't have Linux save for a very frustrating raspberry pi, but I have tried all the flashing things like exe avrdude and Atmega flip, but none of these can even see the mega 32u4.
In device manager it shows consumer vendor defined device and hid input devices, and duplicate numbers of generic USB, but no com port. Even when I press the reset button to initiate the bootloader software.
Quite strange I must say, but I have tried all I currently can (without trying too much)