Hello Derek,
I have a server with a few extra addons as well and the update script has not broken anything so far.
But then you may have some different addons installed then me.
The only thing I changed in the update script are the phpupdate files ... I updated to the latest ones ... php4.3.10 from
http://open.rhx.it/apt/redhat/7.3/i386/rpms.rhx/ ... mind you I just tried that link and it seems to be down atm.
If you need those files let me know and I'll send them to you.
One thing though is yours the 6.01 or the 6.0.1-01 ver.
I'm running the 6.0.1-01 with quite a few exras.
Tib