Some dock icons displayed as grey cog and are unresponsive to start an app, but responsive when app is running

[AlwynBarry]

Issue:

For the past 2 weeks some dock icons are greyed cogs. All my dock icons (bar Nautilus and Cosmic Terminal) are Flatpaks, but the icons for RhythmBox and Geany are greyed cogs, as is the icon for Gnome Terminal. Even if I take them off the dock, then run them, the icon is simply a grey 'cog'. Some other apps are affected, though not all (e.g. FileZilla and Audacious display as grey cogs in the dock, but not Audacity, GIMP or Inkscape - I've not tried all I have installed though!).

These greyed icons are unresponsive to start the programme, but do work as normal (though still not with the correct icon) once the app is started from the launcher. I've tried uninstalling (including all app data) and re-installing, but the same icon is displayed. The launcher has all the app icons in it displayed correctly, and if you use 'Pin to app tray' from the Launcher the correct icon appears, and responds to launch the program, but the grey cog icon appears in addition to the app tray icon and any further program interaction via the dock has to be via the grey cog icon.

How to reproduce:

I don't know - it just happened. I guess there could have been a flatpak update for those apps, but then again Gnome Terminal is also not displaying its icon and it's a system app. Some apps I know have been updated, like LibreOffice, are displaying without any problem. Happy to investigate further if given info on how to do so. Also, happy to 'reset' whatever cache the dock uses to see what happens - just let me know how.

System Details

OS: Fedora Silverblue 40 Compositor: Wayland Desktop: Cosmic Epoch (updated to build 2024-09-17 in the Fedora Cosmic Epoch build (COPR) System: Huawei Matebook, 16Gb, 1Tb SSD (though this is likely irrelevant)