I have a question somewhat related to this topic. My bog standard arduino (2009 flavor) with bootloader uploads just fine with the normal IDE upload command via USB serial. However if I then take my TinyUSB ICSP programmer and use the IDE's file menu "upload using programmer" option then it too burns the sketch fine into the board, however the bootloader gets erased (I checked after burning the sketch by reading flash content with a AVRDUDE standalone GUI program). So how did the fuse setting get changed such that the bootloader code was not protected as it normally gets protected using the standard USB serial uploading?
Lefty