Layers in the linked file is override
When checking your file, you may encounter the following notification: 'Layers in the linked file is overridden'. That doesn’t mean that you cannot use layers within your files, it just means that whenever you make any changes within the file you created it will be reflected in Indesign document e.g. adding a new layer in the linked file will be reflected in InDesign while updating the link.
In order to prevent new layers from appearing in your InDesign document please enable the option below: