diff --git a/pkg/sync/reconcile.go b/pkg/sync/reconcile.go
index dc18eb7d7..550697691 100644
--- a/pkg/sync/reconcile.go
+++ b/pkg/sync/reconcile.go
@@ -76,18 +76,36 @@ func Reconcile(targetObjs []*unstructured.Unstructured, liveObjByKey map[kube.Re
 	managedLiveObj := make([]*unstructured.Unstructured, len(targetObjs))
 	for i, obj := range targetObjs {
 		gvk := obj.GroupVersionKind()
+
 		ns := text.FirstNonEmpty(obj.GetNamespace(), namespace)
-		if namespaced := kubeutil.IsNamespacedOrUnknown(resInfo, obj.GroupVersionKind().GroupKind()); !namespaced {
-			ns = ""
+
+		namespaced, err := resInfo.IsNamespaced(gvk.GroupKind())
+		unknownScope := err != nil
+
+		var keysToCheck []kubeutil.ResourceKey
+		// If we get an error, we don't know whether the resource is namespaced. So we need to check for both in the
+		// live objects. If we don't check for both, then we risk missing the object and deleting it.
+		if namespaced || unknownScope {
+			keysToCheck = append(keysToCheck, kubeutil.NewResourceKey(gvk.Group, gvk.Kind, ns, obj.GetName()))
 		}
-		key := kubeutil.NewResourceKey(gvk.Group, gvk.Kind, ns, obj.GetName())
-		if liveObj, ok := liveObjByKey[key]; ok {
-			managedLiveObj[i] = liveObj
-			delete(liveObjByKey, key)
-		} else {
+		if !namespaced || unknownScope {
+			keysToCheck = append(keysToCheck, kubeutil.NewResourceKey(gvk.Group, gvk.Kind, "", obj.GetName()))
+		}
+
+		found := false
+		for _, key := range keysToCheck {
+			if liveObj, ok := liveObjByKey[key]; ok {
+				managedLiveObj[i] = liveObj
+				delete(liveObjByKey, key)
+				found = true
+				break
+			}
+		}
+		if !found {
 			managedLiveObj[i] = nil
 		}
 	}
+
 	for _, obj := range liveObjByKey {
 		targetObjs = append(targetObjs, nil)
 		managedLiveObj = append(managedLiveObj, obj)
diff --git a/pkg/sync/reconcile_test.go b/pkg/sync/reconcile_test.go
new file mode 100644
index 000000000..d73e79001
--- /dev/null
+++ b/pkg/sync/reconcile_test.go
@@ -0,0 +1,52 @@
+package sync
+
+import (
+	"errors"
+	"testing"
+
+	"github.com/stretchr/testify/require"
+	"k8s.io/apimachinery/pkg/apis/meta/v1/unstructured"
+	"k8s.io/apimachinery/pkg/runtime/schema"
+
+	"github.com/argoproj/gitops-engine/pkg/utils/kube"
+)
+
+type unknownResourceInfoProvider struct{}
+
+func (e *unknownResourceInfoProvider) IsNamespaced(gk schema.GroupKind) (bool, error) {
+	return false, errors.New("unknown")
+}
+
+func TestReconcileWithUnknownDiscoveryDataForClusterScopedResources(t *testing.T) {
+	targetObjs := []*unstructured.Unstructured{
+		{
+			Object: map[string]interface{}{
+				"apiVersion": "v1",
+				"kind":       "Namespace",
+				"metadata": map[string]interface{}{
+					"name": "my-namespace",
+				},
+			},
+		},
+	}
+
+	liveNS := &unstructured.Unstructured{
+		Object: map[string]interface{}{
+			"apiVersion": "v1",
+			"kind":       "Namespace",
+			"metadata": map[string]interface{}{
+				"name": "my-namespace",
+				"uid":  "c99ff56d-1921-495d-8512-d66cdfcb5740",
+			},
+		},
+	}
+	liveObjByKey := map[kube.ResourceKey]*unstructured.Unstructured{
+		kube.NewResourceKey("", "Namespace", "", "my-namespace"): liveNS,
+	}
+
+	result := Reconcile(targetObjs, liveObjByKey, "some-namespace", &unknownResourceInfoProvider{})
+	require.Len(t, result.Target, 1)
+	require.Equal(t, result.Target[0], targetObjs[0])
+	require.Len(t, result.Live, 1)
+	require.Equal(t, result.Live[0], liveNS)
+}