If you want to remove the disk images you created you can go to the folder ~/.local/share/gnome-boxes/images and remove (or move to other folder) its content. But the problem may persist.
Take into consideration that Gnome-Boxex is just the interface for libvirt and qemy. You may uninstall and reinstall those but you can also go to ~/.config/libvirt/qemu/ to check the xml files from there. Each Virtual Machine you add in Boxes will add one more xml file in quemu folder. Earlier, when I started to make a copy of a VM and stopped it before finishing a xml file was added but the image was not copied into the folder, so an error was triggered. As soon I removed the xml file of the intended copy the issue was solved.