You were so close, but I like your initiative.
Change
avrdude -p at90usb82 -F -P usb -c avrispmkii -U flash:w:UNO-dfu_and_usbserial_combined.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
to (at90usb162 for the 16u2)...
avrdude -p at90usb162 -F -P usb -c avrispmkii -U flash:w:UNO-dfu_and_usbserial_combined.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
...or "-c arduino" if you are using Arduino as ISP. I have successfully re-bootloaded my Uno's 16u2 this way.