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There is a current limitation in the application that prevents retaining the theme settings when you load the Checkout page. You should only load the Checkout page view in either Preview Mode during development or before setting any config options. Do not load the Checkout page in Presentation mode if you have configured any theme options or you will lose the settings. You will not be able to preview your options applied to the checkout page in Presentaion Presentation mode at this time.
What options are configurable outside of what is available in the Theme Designer UI?
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