Remove IPSEC Tunnel

You need to resolve those dependencies you can see in the GUI as "Ref" before you can delete an vpn. It must be showing the number of reference. Just click it. Now it should show all of those places where the tunnel is referenced. Some of those paces would have their own dependencies/references. If not '0', click it again to see the references of the references. Then repeat the process until you see '0', then you can remove the reference point. 

And start coming back up from the bottom to remove the entire trees.

But just be careful if those references are referring not only the one you want to remove but something else as well. In that case, you shouldn't remove it completely but removing the particular one from the members of the object. ex) If you have a zone to bind multiple VPNs to use it in just one pair of policy, you need to keep the zone for other vpns but remove the one from the members.