No it's not only css.. that is just the beginning.
You should always use a child theme to prevent this from happening.
Since you all ready have altered twentyten, and it will be overwritten if you upgrade to 3.2.. my suggestion would be to:
1-download your version of twentyten which is currently on your server
2-using the method described above to make a child theme,
rename your twentyten css file to something else:
Theme Name: Twenty Ten Child
Theme URI: http: //example.com/
Description: Child theme for the Twenty Ten theme
Author: Your name here
Author URI: http: //example.com/about/
3- name your current downloaded theme folder to mytwentyten (or whatever works for you)
4- Download the current 3.2 WP to your hard drive, go to wp-content/themes/twentyten
5 - grab that folder and upload to your server in /themes
6 - NOW upload your child (mytwentyten) to your server in /themes
7- go to the dashboard / themes and then click on 'mytwentyten'
This should give you clean version of 2010 and your altered version of 2010. Although this isn't a perfect work around it should work.
The other option would be to make a child theme of Twentyten as described above with only the css file..
but then copy all your changes into the css file and if you changed header.php copy it to your child theme, if you changed functions.php copy it to your child theme.. etc..