pointer disappears in gimp/krita with graphic tablet (wayland)
I have a similar issue, however in my case there's two independent cursors (mouse and graphic table) and the graphic table simply disappears (but somehow moving back and forth different windows it comes back)
https://bugzilla.gnome.org/show_bug.cgi?id=754806
According to this issue, Magnification could cause the cursor to be missing. Do you happen to have it enabled?