nishita your prob is prbably the fact its an initrd kernel.
there are numberous ways around this but I find the most convenient is a small partition for /boot

I let each distro do what it wants and overwrite the MBR then copy the /boot stuff (renaming as appopriate and not copying the symlinks like vmlinuz BUT not forgetting hidden files ...

backup the installed lilo.conf then I find the previous lilo.conf and copy it to /etc and edit it to add the last distro and rerun. (you need to make sure you keep all the correct copies by kernel name)

Once you do this you can use your apt cache to reinstall all the stuff from the other version of kanotix.... (I think /var/apt/cache) Im at work now so hard to be exact!

then I copy the /etc/apt/sources.list
and apt-get upsdate
then run synaptic and see upgradable packages since you might have later version you might prefer.

None of this touches your sacred BH4.... but it should give you everything you want...

another trick is I have a large /shared partition I use as a quasi home.
if you share your home across distros then .kde and other stuff gets messy thus I mount a partition as /home/user/shared for all the non specific stuff... (downloads/docs etc.)