So I got Nick's code working on alternative pins. But just as I suspected, the bootloader is gone now. I'm reading the spec sheet. It seems the chip erase erases the entire FLASH.
Am I understanding this right? IF I use an ISP, Arduino IDE tells avrdude to do erase the FLASH, upload the sketch and then the bootloader. This is the only way that makes sense to me. I'll combine the sketch and bootloader to see what happens.