The Argo CD deletes all in-flight hooks if you terminate running sync operation. The hook state assessment change implemented in this release the Argo CD enables detection of
an in-flight state for all Kubernetes resources including Deployment, PVC, StatefulSet, ReplicaSet etc. So if you terminate the sync operation that has, for example,
StatefulSet hook that is Progressing it will be deleted. The long-running jobs are not supposed to be used as a sync hook and you should consider using
Sync Waves instead.
From here on you can follow the regular upgrade process.
The 1.3 release introduces backward incompatible changes in some public Argo CD APIs. Please make sure to upgrade Argo CD CLI to v1.3.