I do not know how to update. There is no information on the page. The version I have installed with Flatpak is 1.6.1.
Try
flatpak update --user org.libretro.RetroArch
“Updating all your installed applications with FLatpak is a single command: flatpak update It is also possible to update an individual application by adding its name to the command: flatpak update APPLICATION”
On the Flatpak page you will find the information, but in retroarch no http://flatpak.org/command-line.html