I am using Fedora 43 with GNOME 49. When I bought my FW12 (Core i3-1315U) last November the Framework stylus worked perfectly with every app that I used. Recently though some apps don’t seem to register input from the stylus, whether that be clicks or strokes. Krita, for example, tracks the stylus as though it were a pointer, but I can no longer interact with the app at all with the stylus. It doesn’t seem to be a Flatpak issue, as Joplin still allows me to draw notes, and my browser also allows me to interact with my stylus. Other random apps also have this issue, like Protonmail (also installed as a Flatpak).
I have a feeling it might be an X/Wayland related, but I wouldn’t know what would’ve changed since last year for it to have stopped working.