Will I brick my Ender 3 if I try flashing without a bootloader?
My understanding is that if there is no bootloader, you can't flash over USB; you need an ISP programmer attached to the board. So if you're able to flash over USB, that means there is a bootloader, and updating via the bootloader should leave the bootloader in place and just overwrite the rest of the firmware. I'm not sure how strongly this is enforced, though, so you may want to wait for supporting comments/answers from others.
Of course it's always possible to damage your printer in ways that require replacement of the board or at least some parts on it if you flash bad firmware, so you need to be cautious anyway.