As mentioned by Matthias recently in his blog, restarting a flatpak app after an update has become really straight-forward. It sounds like a good idea, so here's a patch series that implements it. For once, using telepathy isn't a pain in the arse, but comes in handy - we can actually restart the application without disconnecting any networks, which makes the restart absolutely seamless.
I'm not entirely sure a modal dialog is the best option though:
Maybe this should be a notification instead?