At the moment, WordPress replaces core files when it updates. This will change in the future, but for now all core files get replaced, i.e. every file that comes with WordPress. This includes the default twenty ten theme.
If you modify twenty ten you should save your modified theme with a different name. To do this, make a copy of the twentyten folder and rename this folder. Then, inside the renamed folder open styles.css and change the line Theme Name: Twenty Ten to Theme Name: Same Name as your Renamed Folder. Add this folder back into wp-content/themes and activate it in your admin settings.
When WordPress updates it leaves your own themes alone, so you won’t lose the changes you made.