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 an automated sync starts right before a sync window closes, the sync operation stays ongoing but gets paused, with sync status saying "Sync operation blocked by sync window". If the sync is attempted to be terminated, it stays stuck in Terminating state, until sync window opens again.

To Reproduce

Given an example current time of 11:00:00, create a sync window with allowed manual sync that closes at 11:01:00. At 11:00:30, apply the application.yaml from this repo which ensures a slow sync: https://github.com/puskunalis/argocd-sync-window-bug.

Auto-sync (important - manual sync does not run into this issue) should begin before 11:01:00, and while the sync operation is ongoing, you will observe that the sync status reports "Sync operation blocked by sync window".

Attempt to terminate the sync, observe that it stays in this state and is not terminated.

Additionally, attempt to delete the application, observe that it is not deleted.

Expected behavior

Upon clicking terminate sync, the sync gets terminated and a manual sync is possible to be made due to a setting on the sync window allowing manual syncs. Additionally, there could be an option that allows a sync that started before the sync window closes to finish successfully without being stopped. Currently, the only option to get the sync unstuck is to modify the sync window to be opened.

Screenshots

Version

We observed this on previous versions as well, v3.1 and v2.x.

argocd: v2.12.4+27d1e64
  BuildDate: 2024-09-26T09:31:42Z
  GitCommit: 27d1e641b6ea99d9f4bf788c032aeaeefd782910
  GitTreeState: clean
  GoVersion: go1.23.1
  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

I could work on the PR for this if we confirm that this is not the expected behavior.