Jan-Michael has recently changed Epiphany Technology Preview to use a separate app ID. Instead of org.gnome.Epiphany, it will now be org.gnome.Epiphany.Devel, to avoid clashing with your system version of Epiphany. You can now have separate desktop icons for both system Epiphany and Epiphany Technology Preview at the same time.
Because flatpak doesn’t provide any way to rename an app ID, this means it’s the end of the road for previous installations of Epiphany Technology Preview. Manual intervention is required to upgrade. Fortunately, this is a one-time hurdle, and it is not hard:
$ flatpak uninstall org.gnome.Epiphany
Uninstall the old Epiphany…
$ flatpak install gnome-apps-nightly org.gnome.Epiphany.Devel org.gnome.Epiphany.Devel.Debug
…install the new one, assuming that your remote is named gnome-apps-nightly (the name used locally may differ), and that you also want to install debuginfo to make it possible to debug it…
$ mv ~/.var/app/org.gnome.Epiphany ~/.var/app/org.gnome.Epiphany.Devel
…and move your personal data from the old app to the new one.
Then don’t forget to make it your default web browser under System Settings -> Details -> Default Applications. Thanks for testing Epiphany Technology Preview!