Ignore this, nothing to see here, move along. Spurious PEBKAC interrupt detected.(Note to self: Engage brain for more than 0.3 seconds before posting).
Proceed directly to osor's post below.
echo -e "\n" | dd bs=1 count=1 of=$file seek=$(( $(stat -c %s $file) - 2))
I'm assuming you want to retain the newline, this replaces the last two bytes (i.e. "%\n") with "\n".