Sorry! Thought I had responded after your post on the 24th. Yes, it sounds like one board is the older revision- if I remember correctly the only release versions are 3 and 4, which will be silk screened on the PCB in very small font near the 32 pin connector. Rev 4 adds the battery voltage divider, as well as the bootloader change to display text. The voltage divider is just that- two 1M ohm resistors in series from the battery to ground, with the center tap connected to an analog pin. This results in pretty minimal current draw while allowing the ADC to still get a reasonable reading.
There shouldn't be a direct problem preventing updating the bootloader from a user program, but there wouldn't be any backup without being able to reflash with an external programmer- an error would probably brick the board, but there should not be an error
. I can look into this shortly if you're interested in trying it.