I've used redhat for many releases. The machine I'm on (unfortunately) need to support win98 as well as redhat. I've been using a third party boot manager and have installed lilo in the linux partition (/dev/hda3). After installing 6.1 in update mode, the lilo.conf file specified that it would boot from /dev/hda. As as result, the update overwrote the boot manager and destroyed access to the windows partition. With a little work I was able to recover the bad partition and reconfigured lilo to properly place the boot routine. This could really sour a beginner if they are trying to maintain two systems on their PC.
The issue of running lilo configuration during an upgrade is resolved with the latest boot disks and update images available from the errata website. This will allow you to specify the location of lilo during an upgrade, just as you are able to do during the installation.