I don't know if a bootloader would corrupt during a custom ROM Flashing in Samsung...^by having a failure while flashing it such as purposely pulling out your battery during the process.
AFAIK, it gets corrupted if you pull out battery while flashing an Hboot file... updating it's FIRMWARES..
Custom ROM files writes partitions which can be reformatted if your bootloader is alive...
It's like you are installing windows and suddenly light goes off so you just format HDD and reinstall...
Bootloader is like Bios of phone.. just like if your PC turns off during a bios flash, then it's mobo is completely dead, same can happen with phone..
Flashing Official Roms via RUU can corrupt bootloaders if stopped in middle as they mostly contain firmware packages aswell...