Created attachment 106403 [details] tray icon and discover before flatpak update from konsole tray icon says 1 update is available, but discover shows no update (see the screenshot). "flatpak update" command on konsole found and installed some updates (see the screenshot). After the update process from konsole, the tray icon gave me the correct information (system up to date). See the screenshot. I use Arch, discover 5.10.3.
Created attachment 106404 [details] flatpaks updated from konsole
Created attachment 106405 [details] tray icon after update from konsole
I can confirm, this is caused by discover not listing related refs (e.g. localization). I'll add support for this as soon as possible.
Fixed in 5.11. Commit: https://cgit.kde.org/discover.git/commit/?id=a9a018589de58115124e60abd72a048cd34ef14e