By default, ArgoCD doesn't remove resources if the manifests are deleted, but you can switch this by turning on auto prune[1]. Likewise, you can specify whether a persistent volume should be retained or deleted if the k8s PersistentVolume resource is deleted[2]. Both of those settings would have prevented data loss in this case, but of course that's easy to say in hindsight.

[1] https://argo-cd.readthedocs.io/en/stable/user-guide/auto_syn...

[2] https://kubernetes.io/docs/concepts/storage/persistent-volum...