Hi Joshua,
CaseComplete should be preserving the color formatting of the text when you generate reports. In other words, the generated report should be using the color you specified within CaseComplete automatically. If that's not happening for you, would you mind sending an email to support@serlio.com so we can track this issue and see if there's a defect that you've uncovered?
And since you're interested in tracking changes, you may be interested in our new requirements collaboration tool, Requirements.cc. It's still in beta, but by using CaseComplete 2011 (and later), you can upload, share, collect feedback, track changes and more on your projects in an online environment. If this sounds like something that might be useful to you, you can read about it on our blog page: http://blog.requirements.cc/
Hope this helps. Let me know if you have any questions or need addtional information with any of this.
Regards,
Jeff