Some default Wordpress or Woo templates can be created only once, and they can’t be deleted (only reset). E.g. once “Product Search” or “Product Catalog” templates are added, then the same type template can’t be added again. There’s no such selection anymore.
Duplicate Template button allows duplicating such unique templates, and then WP may start to act unpredictable. E.g. visibility conditions may be ignored for primary and copy templates. Sometimes content of copy template may just gone etc. In short, it looks like there is a reason from the WP team side why some default templates can’t be created twice.
Solution. “Duplicate” button should be disabled for such types of templates, or when duplicate is made, copy should be completely converted to custom template type.