A while back I referred to this in passing in a thread here — I kept finding that my custom tool panel (Character + Paragraph + Text Frame + Transform) would vanish unexpectedly. I'd have to reassemble the custom panel all over again. But it wasn't a bug after all — they didn't "just vanish."
I use Alt+F4 to exit Affinity Publisher. But it turns out the program has been using the keystrokes to close the front-most window, which always seems to be that custom tool panel. Using the keyboard shortcuts feature to bind Alt+F4 explicitly to the Exit command has fixed this. Alt+F4 no longer affects the custom tool panel.