There is a possibility that the bootloader routine got overwritten accidentally, so you would have to program another one by using a programmer. Sometimes it happens, since bootloader code is kept in the flash memory, along with your code and if the code accidentally writes something in that area or the content gets damaged by other means, bootloader stops working. Second reason could be a hardware fault. Try the bootloader on another PC too, if possible.
If you use the mE bootloader to upload a hex, it won't touch the bootloader itself, it is made to take care of that, but if your code messes with the memory, or uses specifically set memory locations to store variables or other data, it can damage the bootloader code. Avoid declaring variables on predetermined addresses and flash-write functions and you should be fine...
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