Thanks. =)
Currently CAT only uses the INI files, so it loads them, and rewrites them. So if they get overwritten, then CAT would use the new values.
My server settings never get rewritten when updating, so... I'm not sure what is happening there with your settings files. I assume you've read the CE forums to see if there is a way around this? Like I said, I've never had that problem.
However, regardless of what my settings do or don't do, you're having a problem. =) I'll see what I can do about backups and reloading settings, etc. It won't be in this version, but the new version is paving the way for me to start doing other things. So, I'll do something that should help you out soon. =)