Comment by Kamil Maciorowski on What is it about the `shutdown` command that displeases Kate (KDE Advanced Text Editor)?

For me Kate saves its bookmarks in ~/.config/katemetainfos. In your case, how is the filesystem holding this location mounted? I can imagine e.g. if your .config was in FUSE then the user process providing the filesystem would get SIGTERM and exited, not waiting for Kate to update the file.