Ok I found the answers to this and by the looks of a few different places and forums im not the only person that has or will face this problem.
When installing the security update RaQ4-All-Security-2.0.1-15959.pkg on a cobalt RAQ 4 that particular pkg file accesses a few libraries on the server. Normally this is fine but if you have installed a pkgmaster version of php on your machine this updates goes horribly wrong. You will find that your web interface no longer works along with ftp and ssh.
To fix this you must telnet into your box.
(Hope you left the telnet server on before you did the update!!)
Do the following commands . . .
[FONT=times new roman]
1.)log into telnet to your Raq
2.)type "su -" then type your admin password
3.)type "cd /usr/lib"
4.)type "ln libgd.so.1.8.4 libgd.so.1"
5.)type "ln libgd.so.1.8.4 libgd.so"
If you get the following error:
[root lib]# ln libgd.so.1.8.4 libgd.so
ln: libgd.so: File exists
Then type: "mv libgd.so libgd.soold" then repeat #5
6.)type "/etc/rc.d/init.d/httpd restart"
[/FONT]
After doing this your web servers will be back online but your version of php and your sessions will be poooched. The best thing to do now is to uninstall the pkgmaster version of php (currently PHP Release 4.1.2-3 ) then reinstall it with a fresh copy from their site. Here is how to uninstall on a cobalt.
[FONT=times new roman]
1) Telnet into your machine as admin.
2) Type "su" to login again as the super user and enter your admin password
3) type "cd /var/lib/cobalt/uninstallers" without quotes
4) type "ls" and find your uninstall file.
5) type "./filename"
6) After a few moments you will be returned to the prompt and all is fixed. Type "exit" and press [ENTER] twice and your out of the telnet session
[/FONT]
And that's it! When I did this everything is functioning the way it should and the security updates are in place. And if they come out with another update these steps should work fine to fix it again.