When deleting a layer, you have the option to delete the content and markups contained within the layer or move this information to the base PDF.
If you just want to conceal a layer and its content from view, see Using Layer Visibility.
Alternatively, right-click the layer and select Delete.
To delete the markups on
Note: Unchecking both boxes will delete the definition of the layer and keep all content and markups by moving them to the base PDF.