As ProThoughts said, the version number is defined at the top of 'qa-include/qa-base.php'. We use semantic versioning, so for custom versioning you should add a dash then whatever you want.
For example if you're on 1.7.4, change the version to '1.7.4-v2' then increase to v3, v4 and so on.
Normally changing core code is not recommended, but in this case it's fine to lose your changes. A new version will change it again, e.g. to 1.7.5 or 1.8.0. Then if you change the CSS again later you can use '1.8.0-v2'.
The other option as you say in your answer is to override the appropriate function in the theme. This is probably better, especially if you have a build process that auto generates files.