At application level

Disable autoSync

The first thing to consider is disabling autoSync. This will make argocd not doing anything in the application resources when some changes in the target state. In order to do that disable that section in the application definition

spec.syncPolicy.automated

Prevent individual Resources

We can protect a kubernetes resource managed by argocd to be deleted using the following annotation in the resource

metadata:
  annotations:
    argocd.argoproj.io/sync-options: Delete=false

Also, we can protect a kubernetes resource managed by argocd to be pruned using the following annotation in the resource

metadata:
  annotations:
    argocd.argoproj.io/sync-options: Prune=false

This option only has sense with autoSync and prune enabled when definig the application

spec:
  syncPolicy:
    automated:
      prune: true

In both cases, Prune=confirm requires manual confirmation before deletion/pruning