Maybe some clues here: see updates to rev 1.05
http://www.pjrc.com/teensy/loader.htmland more
here:
Hi guys! Here's the EEPROM-writing asm code the GUI-based Teensy Loader
uses. Actually, a binary copy of this is built into the Teensy Loader.
When opening the .hex file, the Teensy Loader checks if there's an .elf
file which matches the .hex file, and if so the .eeprom section is
extracted from the .elf and appended to the binary data from of tiny
program. Once downloaded and run, it just writes to the eeprom and then
jumps back to the bootloader.
Seems you need the original elf, or a way to put them back together.