A course theme design can be changed for an existing course.
Double-click the course in the course panel to open Properties. Click the Themes tab, pick a new theme, and click Update.
Keep in mind that some themes (particularly custom themes) may have placeholders in different positions or other custom styling. These elements may need to be fixed on existing pages when you switch themes if you want the pages to match the new theme design.
Note: If you have copied a course for re-use (see Copy a course) the theme designs are unique even though the re-used Learning Objects are shared. This means you can brand course content differently using different themes, for example, but still keep the content synchronized.