The wp-content/themes/default files would have been upgraded in the automatic upgrade so if you put your theme files in that folder they would have been overwritten with the standard version of that theme.
You may need to restore a backup of your theme folder.
You might consider changing your theme to something besides default so that doesn’t happen in the future.
Thanks for the tip. I started using “default” as the name of my custom theme because I was having a little problem where my WordPress would revert back to the default theme for reasons that are still unclear. Having my custom theme named “default” seemed to solve this, because it would just revert back to my custom theme. Now I’ve either got to test 2.8 for a week or so to find out if I’ve still got the problem with reverting back to default, or I’ve got to find a different work-around.
If I remember correctly there was some work on that ‘reverting back to default’ theme issue, but usually when that happens (reverting to default theme) it is a sign of something wrong in the code of the currently active theme.
To change the name of the theme make sure you change it in style.css (look for Theme Name: WordPress Default and change it to something unique) and also change the name of the directory (folder). If you don’t change both you risk having your customised theme overwritten whenever you upgrade WordPress.
