qvm-prefs -l <vm-name>
Then, change the the template property (not the root_img property) for each of the VM's:
qvm-prefs -s <vmname> template fedora-25
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Now, the only question left - how to remove "Template:fedora-23" from the Applications menu?
sudo xdg-desktop-menu uninstall fedora-23-vm.directory fedora-23-qubes-appmenu-select.desktop
Those latter two identified by looking in the directory you specified, /etc/xdg/menus/applicaitons-merged and reading the fedora-23-vm.menu file.