Ahh, I understand. When you change the user who is excuting CGI for the domain, then the place where the apache server looks for the files changes to the new user directory - however the files arn't copied over or anything. So you change the CGI user and the site dies.
There are two easy things to do here. First just switch the CGI back to user A - it doesn't make and difference in the site (enless you've installed custom stuff for that user like webmail or php5)
Or seconed, copy all of the site files from User A to user B by loging in to FTP with user A's info - download all the site files to your hard drive, then log into FTP with user B and upload to the new site directory.