I have an Ubuntu running Apache and OScommerce to service my website. Over several months, several updates and patches are stacking up in my update area. Back in January when I initially set up this server, I performed the automatic updates. This basically brought the server to it's knees with slow performance that it could not recover from. I had to do a total reinstall of the server. Of coarse now it is requesting to install these updates again and I am very reluctant to do so. I'm thinking a safe approach might be to shut off Apache and Oscommerce during the update. Any suggestions?

Thanks in advance