Okay, so the runtimes were fine, good to know. Btw, you can remove runtimes without first removing the apps that depend on them. They just won’t work any more until you install it again.
I wonder if there is a clean way to thoroughly remove all and everything coming from Flatpak. At this point I don’t even care if there is any data lost …
Not an official one, but this should do the trick if you really want to delete everything. If you want to, you could back up the user files for your other Flatpaks first.
If that also doesn’t work, I’m 95% certain it has to be one of your system packages. Weird that a system package would break any Flatpaks though… What distro are you using anyway?