I had a similar problem, I did this, everything is back on track!
pkcon refresh Refreshing cache Waiting in queue Waiting for authentication Waiting in queue Starting Refreshing software list [root@Jolla nemo]# pkcon upgrade Command failed: Option 'upgrade' is not supported [root@Jolla nemo]# pkcon update Getting updates Waiting in queue Starting Querying Refreshing software list No packages require updating to newer versions.