I applied FP 3 to 10.2.1 and it removed our company's logo from the welcome page. Anybody knows which xml file it is? It used to
be system.xml in earlier versions.
After applying a fix pack to your installation, most files will revert back to their original configuration as that is a part of the Fix Pack.
I may not be able to answer your question, but a good idea for the future is to document every change you do to all files in the Cognos directories so that after applying a fix pack, you or someone on your team is able to revert your environment back to looking and feeling the way that it was before the Fix Pack (that is unless they make a significant change to the layout or how the files in the background work)
Your are correct but I started here 2 months ago :)
I'm new to Cognos as well, but I know one thing about all software: You can count on an update replacing all core content. Rather than modifying a built-in skin, it is better to create a new one with your company's styles and logos.