I have developed bootloader code using ATMEGA64a, its working fine, but i do have one doubt what if worst case bootloader gets corrupted then is there any way to flash bootloader.
You should make it sure in your bootloader that it will not overwrite it.
Lock the bootloader to prevent it from unintentional write instruction from the application code.
Set brown out reset to prevent flash corruption due to low voltage.
I hope you really means bootloader corruption and not a bootloader BUG....