In theory a Knoppix style regenerates everything but actually not, passwords stay, fstab is normally regenerated but you can override this by including the nofstab cheatcode in the lilo append= line. xf86config-4 only overwrites if an existing one is not found so it stays as is. However, since you are on HD the old configs are still there until they are overwritten by the startup script so it shouldn't be necessary to overwite everything, hdware setup is still the same, etc. so I have eliminated regenerating ld.so.cache & modules.dep to speed up startup.

A debian style install might have been a better choice but I did the Knoppix style because I wanted to make a remaster from it. You can make a remaster from an operating knoppix style system instead of fiddling about with chrooting into a special system, I wrote a how-to...

Now this system have been running for some time, it has been extensively customized, I don't want to reinstall, so I'm just tweaking a bit.
I usually tweak 'til it's broken, just wondering if it's going to break sooner or later.