Site Navigation Templates can only be successfully applied to Sites where you are not currently logged in.
To apply the Template to the site you are working in, “Site A”, for example:
Switch sites into a different site on the enterprise
Go to Enterprise on the Navigation Bar
Select Manage Sites
Select the desired Site Navigation Type from the drop-down menu
Select the site where you want to apply a Site Navigation Template; "Site A"
Click Apply Template
"Are you sure you want to create new Navigation bar for all selected sites?"; Click Yes
"New Navigation bar has been successfully set." Click OK
When you switch back into “Site A”, the Navigation Bar will match the template.