UPDATE: migrating the flatpak by simply updating now works for me. End up with the minetest dir symlinked to the new luanti dir. No idea what fixed it.

Looks like 5.12.0 is only available as a flatpak under a new ID: org.luanti.luanti. The old net.minetest.Minetest has stopped at 5.11.0

https://github.com/flathub/net.minetest.Minetest/issues/103

Flatpak should prompt you to migrate to the new ID when you update, however this didn’t happen for me.

https://docs.flathub.org/docs/for-app-authors/maintenance#end-of-life-rebase

Could be some version of this bug:

https://github.com/flatpak/flatpak/issues/5819

Has anyone else managed to migrate to org.luanti.luanti ok?