You can kill the bootloader of your Leonardo/ Pro micro if you program it with some Linux IDE!
Please consider this issue:
The solution is to remove/disable the modemmanager that interferes with the burning process.
I have now 3 embeded ProMicro boards that do not respond any more to serial.
I have probably got no way to restore their bootloader without desoldering them... 
Why desoldering them? If it is just bootloader it can be uploaded back via ISP. Neither new chip has a bootloader.
Budvar10:
Why desoldering them? If it is just bootloader it can be uploaded back via ISP. Neither new chip has a bootloader.
Desoldering the board, not the chip.
SPI is used...