Atmel atmega32u4 not recognized when connected by usb after attempting to flash new bootloader
You cannot load the bootloader over USB, that job needs to be done with an in-serial-programmer (ISP).  You could have stopped the board working if you wrote the wrong fuses, e.g. different clock frequency.

Flashing the bootloader via ISP can be done with the Arduino IDE and there are lots of tutorials on the web.  Try it, will probably work for you.