I have a feature I've created named appcat_application_content, which defines an "Application" content type. When I created the feature, it autodetected several taxonomies referenced by fields that are term reference fields using those taxonomies.
After initially creating the feature, I realized that I wanted to create a separate module for defining my taxonomies, because the taxonomies are also referenced by other content types on my site. I therefore temporarily disabled the appcat_application_content, created and enabled a new feature named appcat_taxonomies that defines all my taxonomies, and then rebuilt and re-enabled the appcat_application_content feature.
When I do this, however, the appcat_application_content says it has been "overridden." The issue is that Features insists on continuing to export taxonomy definitions as part of appcat_application_content and creating a file named appcat_application_content.features.taxonomy.inc. It does this even though the appcat_taxonomies already defines my taxonomies.
The only way I've found to get around this is to create a new, separate feature rather than rebuild the appcat_application_content feature. For example, I can disable appcat_application_content and create a new feature named appcat_application_node. If I do this, the appcat_application_node feature does not include a .features.taxonomy.inc file, which is what I want so that there is no longer an "overridden" issue or a conflict with the appcat_taxonomies feature.