ArgoCD does not detect key removal or container reduction in ConfigMap / Secret / Deployment

[yilas]

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

When reducing a manifest (e.g., removing a key in a ConfigMap or Secret, or removing a container from a Deployment), ArgoCD does not detect any difference between Git and the cluster.
The application stays Synced, no diff is shown, and no update is applied to Kubernetes.
Even worse, the removed part remains in the live object.

To Reproduce

1. Create a ConfigMap and sync it with ArgoCD:

   apiVersion: v1
   kind: ConfigMap
   metadata:
     name: test-configmap-001
   data:
     test-1.json: |-
       { "description": "Test ConfigMap to diagnose Argo sync issues" }
     test-2.json: |-
       { "description": "Test ConfigMap to diagnose Argo sync issues" }

2. Commit and push → ArgoCD creates the ConfigMap correctly

3. Modify the manifest by removing one key

   apiVersion: v1
   kind: ConfigMap
   metadata:
     name: test-configmap-001
   data:
     test-1.json: |-
       { "description": "Test ConfigMap to diagnose Argo sync issues" }

4. Commit and push again

5. Observe in ArgoCD

   1. The application remains Synced
   2. No diff is shown in the UI
   3. The cluster-side ConfigMap still contains the deleted key (test-2.json)

6. Similar behavior occurs with:

   1. Secrets (removing data keys)
   2. Deployments (removing containers from spec.template.spec.containers)

Expected behavior

• ArgoCD should detect that the manifest in Git is smaller (a key or container was removed) or is changed.
• The application should become OutOfSync.
• A sync or auto-prune should delete the missing fields or containers in the live object.

Screenshots

• LIVE MANIFEST

• DIFF

• DESIRED

Version

❯ argocd version
argocd: v3.1.8+becb020
  BuildDate: 2025-09-30T16:04:21Z
  GitCommit: becb020064fe9be5381bf6e5818ff8587ca8f377
  GitTreeState: clean
  GoVersion: go1.24.6
  Compiler: gc
  Platform: linux/amd64
argocd-server: v3.1.8+becb020
  BuildDate: 2025-09-30T16:04:21Z
  GitCommit: becb020064fe9be5381bf6e5818ff8587ca8f377
  GitTreeState: clean
  GoVersion: go1.24.6
  Compiler: gc
  Platform: linux/amd64
  Kustomize Version: could not get kustomize version: exec: "kustomize": executable file not found in $PATH
  Helm Version: v3.17.3+ge4da497
  Kubectl Version: v0.33.1
  Jsonnet Version: v0.21.0

Version of ArgoCD server : v3.1.0 (but we have the same behavior with version 2.14.9)

[choejwoo]

Hello, thank you for creating this issue.
I’ve been testing it in my environment as well, but I have a few questions.

1. In scenario 5, even after performing a Sync, does the ConfigMap data not get pruned?
2. If you are currently using the Legacy Diff(default method), could you try applying the Server-Side Diff as described in the documentation?

Please check when you have a moment. It would be helpful for resolving this issue. Thank you!