Hi,
It is bit difficult to say what could have caused the IAP's to land in to this state.
However, I can suggest the following:
1. While upgrading the IAP's, there is an option "Reboot AP's after upgrade".
The above option is enabled by default. You can uncheck this option & then click on the option "Upgrade Now"
We can easily check the state of each IAP by executing the following commands on the VC:
show upgrade.
Once this output shows that all the IAP's have been upgraded, you can just execute the command:
reload all
Note: There was an issue seen with upgrading IAP's using the local file option (Web UI) which got fixed in 4.2.4.6
So, not sure if you could have been impacted by that.