Checklist:

• I've searched in the docs and FAQ for my answer: https://bit.ly/argocd-faq.
• I've included steps to reproduce the bug.
• I've pasted the output of argocd version.

Describe the bug

Deleting a resource in an Application generated by an ApplicationSet with Progressive Syncs enabled triggers an infinite sync loop.

In the following clip, I initially have 1 deployment and 2 configmaps in my Application. I refresh the application to a new commit, removing one configmap:

To Reproduce

1. Apply the following ApplicationSet:

apiVersion: argoproj.io/v1alpha1
kind: ApplicationSet
metadata:
  name: 'app'
  namespace: 'argocd'
spec:
  goTemplate: true
  goTemplateOptions: [ 'missingkey=error' ]
  generators:
    - git:
        repoURL: 'https://github.com/skwair/argocd-issue-25444.git'
        revision: 'HEAD'
        directories:
          - path: 'overlays/*'
  template:
    metadata:
      name: 'app-{{ index .path.segments 1 }}'
      labels:
        env: 'prod'
    spec:
      project: 'default'
      source:
        repoURL: 'https://github.com/skwair/argocd-issue-25444.git'
        targetRevision: 'HEAD'
        path: '{{ .path.path }}'
      destination:
        server: 'https://kubernetes.default.svc'
        namespace: 'app-{{ index .path.segments 1 }}'
      syncPolicy:
        syncOptions:
          - 'CreateNamespace=true'
          - 'ServerSideApply=true'
  strategy:
    type: 'RollingSync'
    rollingSync:
      steps:
        - matchExpressions:
            - key: 'env'
              operator: 'In'
              values: ['prod']
          maxUpdate: 1

2. Remove any resource from any generated Application in Git
3. Commit and push
4. Trigger a sync via the UI (or wait for applications to refresh)

Expected behavior

To be honest, I'm not 100% sure what to expect since the RollingSync documentation states:

RollingSync will force all generated Applications to have autosync disabled.

Does it include automatic pruning?

Either way, if documentation implies automatic pruning is also disabled, I would expect the Application to simply sync once and mark deleted resource as deleted in Git, but kept in Kubernetes. Otherwise, I would expect Argo CD to prune these resources.

Key observations:

• By default, prune seems to be disabled
• Removing a resource triggers an infinite sync loop (the bug)
• Explicitly setting automated.prune: true (despite documentation mentioning automated is disabled when using Progressive Syncs) on generated Applications fixes the issue
• Similarly, adding the PruneLast=true sync option on generated Applications fixes the issue
• Manually syncing (via the UI or using the CLI) with the prune option also works
• selfHeal seems to always be active and works as expected

Is the official way of enabling automatic resource pruning when using Progressive Syncs setting either automated.prune: true or PruneLast=true?

Version

argocd: v3.2.0+66b2f30
  BuildDate: 2025-11-04T19:52:35Z
  GitCommit: 66b2f302d91a42cc151808da0eec0846bbe1062c
  GitTreeState: clean
  GoVersion: go1.25.3
  Compiler: gc
  Platform: darwin/arm64
argocd-server: v3.2.0+66b2f30
  BuildDate: 2025-11-04T14:51:35Z
  GitCommit: 66b2f302d91a42cc151808da0eec0846bbe1062c
  GitTreeState: clean
  GoVersion: go1.25.0
  Compiler: gc
  Platform: linux/arm64
  Kustomize Version: v5.7.0 2025-06-28T07:00:07Z
  Helm Version: v3.18.4+gd80839c
  Kubectl Version: v0.34.0
  Jsonnet Version: v0.21.0

Logs

These are the logs that get infinitely spammed when the sync is triggered:

{"applicationset":{"Namespace":"argocd","Name":"app"},"level":"info","msg":"generated 3 applications","time":"2025-11-29T10:50:28Z"}
{"applicationset":{"Namespace":"argocd","Name":"app"},"level":"info","msg":"ApplicationSet app step list:","time":"2025-11-29T10:50:28Z"}
{"applicationset":{"Namespace":"argocd","Name":"app"},"level":"info","msg":"step 1: [app-tenant1 app-tenant2 app-tenant3]","time":"2025-11-29T10:50:28Z"}
{"applicationset":{"Namespace":"argocd","Name":"app"},"level":"info","msg":"Application allowed to sync before maxUpdate?: map[app-tenant1:true app-tenant2:true app-tenant3:true]","time":"2025-11-29T10:50:28Z"}
{"applicationset":{"Namespace":"argocd","Name":"app"},"level":"info","msg":"end reconcile in 316.122392ms","requeueAfter":180000000000,"time":"2025-11-29T10:50:28Z"}
{"allPaths":["base","overlays","overlays/tenant1","overlays/tenant2","overlays/tenant3"],"level":"info","msg":"applications result from the repo service","pathParamPrefix":"","repoURL":"https://github.com/skwair/argocd-issue-25444.git","revision":"HEAD","time":"2025-11-29T10:53:28Z","total":5}