Whenever I "dnf update", GNOME Software still thinks that I have those packages waiting to be installed as updates and nags me about them. PK should have some hook to check when updates have been applied on the commandline?
We moved the upstream bugtracker to GitHub a long time ago. If this issue still affects you please re-create the issue here: https://github.com/hughsie/PackageKit/issues
Sorry for the impersonal message, and fingers crossed your issue no longer happens. Thanks.