ok, i was thinking about this during work. if you take time to set it up correctly, then this should work.
say you reapply the b13 upgrade file and hijack. the next step is to use wfaulk's preinit ftp script, with the additions of mkdir /programs0 and /programs1 (so it will automount right afterwards). in /programs0/preinit.d, have a M99reupgrade shell script that checks if a certain file is in the root partition. if not, it copies whatever needs to be in the partition(index.html, rsync, libraries, ntptime, modified mtab/fstab, etc.) and the file that it will check for next time. last command is a reboot -f, and then thats it. you're back to what you were before you reflashed. the problem is that you have to keep track of what you modify in the / partition. what i've done is just have /programs0/base with all files, and do a cp /programs0/base / -r.
sound good?