Steps: 1. Install Firefox and Thunderbird apps, 2. Add both apps to Favorites panel in Kickoff launcher, 3. Try to change Firefox and Thunderbird icons' order, for example to 1st and 2nd place, 4. Try upgrading one of or both apps. Expected result: Firefox and thunderbird icons remain with the same order in Favorites panel. Observed result: Firefox and thunderbird icons disappear from Favorites panel, and after logout then relogin they reappear but their order is changed to last places.
Are these apps native packages, or Flatpaks, or snaps? What distro are you using?
(In reply to Nate Graham from comment #1) > Are these apps native packages, or Flatpaks, or snaps? > > What distro are you using? They are native packages installed using pacman on Manjaro.
I've seen the Firefox icon disappear on KDE Neon User ed. and right now on Neon Testing. It hasn't changed position, but I didn't have Thunderbird installed. I see the correct Firefox icon on Fedora 42 and Solus (git-master). Both FF and Thunderbird (native packages) keep their position in Favorites.