Design atoms not added to appsdesign.xml
You have a component with design atoms. Upon modification of these design atoms, you notice that your appsdesign.xml is not getting updated.
Delete the componentHierarchy page under your template, and request a page that uses that template (which includes your component).
appsdesign.xml is updated the first time when a component that has design values is included in a template. Therefore, if you update your design atoms in your component, then appsdesign.xml is outdated.