If you have a second Arduino you can use it to re-load the bootloader if it gets damaged by the process.
No I haven't, but I like the concept. Any smart keywords to Google for?
First link is http://arduino.cc/en/Tutorial/ArduinoISP
One step they forget to mention is disabling auto-reset on the Arduino being used as an ISP.
Also: optiLoader is a sketch that contains several versions of the optiboot bootloader (like on the UNO) which will program a fresh bootloader onto another Arduino without needing a PC.
I looked at the makefile and it looks like it doesn't do a Chip Erase or change the flag/lock bytes so it should be safe for your bootloader.
Ah that sounds good!
Just for me to learn a bit more from this, are these simple keywords I can check for myself too in Makefiles or are there pitfalls and do I need a lot of experience?
It's not very easy to see. What you are looking for is the 'avrdude' command line options for Chip Erase (-e) or fuse setting (-U efuse, hfuse, lfuse, lock). If none appear it is likely that the makefile is NOT asking avrdude to do anything but write the application (non-boot) FLASH.