diff --git a/internal/controller/argo.go b/internal/controller/argo.go
index a25fa0e20..793913b80 100644
--- a/internal/controller/argo.go
+++ b/internal/controller/argo.go
@@ -21,6 +21,7 @@ import (
 	"fmt"
 	"log"
 	"os"
+	"slices"
 	"strconv"
 	"strings"
 
@@ -961,3 +962,25 @@ func updateHelmParameter(goal api.PatternParameter, actual []argoapi.HelmParamet
 	}
 	return false
 }
+
+// syncApplicationWithPrune syncs the application with prune and force options if such a sync is not already in progress.
+// Returns true if a sync with prune and force is already in progress, false otherwise
+func syncApplicationWithPrune(client argoclient.Interface, app *argoapi.Application, namespace string) (bool, error) {
+	if app.Operation != nil && app.Operation.Sync != nil && app.Operation.Sync.Prune && slices.Contains(app.Operation.Sync.SyncOptions, "Force=true") {
+		return true, nil
+	}
+
+	app.Operation = &argoapi.Operation{
+		Sync: &argoapi.SyncOperation{
+			Prune:       true,
+			SyncOptions: []string{"Force=true"},
+		},
+	}
+
+	_, err := client.ArgoprojV1alpha1().Applications(namespace).Update(context.Background(), app, metav1.UpdateOptions{})
+	if err != nil {
+		return false, fmt.Errorf("failed to sync application %q with prune: %w", app.Name, err)
+	}
+
+	return true, nil
+}
diff --git a/internal/controller/pattern_controller.go b/internal/controller/pattern_controller.go
index a7230d8b8..cd11898de 100644
--- a/internal/controller/pattern_controller.go
+++ b/internal/controller/pattern_controller.go
@@ -162,7 +162,14 @@ func (r *PatternReconciler) Reconcile(ctx context.Context, req ctrl.Request) (ct
 
 	// -- GitOps Subscription
 	targetSub, _ := newSubscriptionFromConfigMap(r.fullClient)
-	_ = controllerutil.SetOwnerReference(qualifiedInstance, targetSub, r.Scheme)
+	operatorConfigMap, err := GetOperatorConfigmap()
+	if err == nil {
+		if err := controllerutil.SetOwnerReference(operatorConfigMap, targetSub, r.Scheme); err != nil {
+			return r.actionPerformed(qualifiedInstance, "error setting owner of gitops subscription", err)
+		}
+	} else {
+		return r.actionPerformed(qualifiedInstance, "error getting operator configmap", err)
+	}
 
 	sub, _ := getSubscription(r.olmClient, targetSub.Name)
 	if sub == nil {
@@ -176,7 +183,20 @@ func (r *PatternReconciler) Reconcile(ctx context.Context, req ctrl.Request) (ct
 			return r.actionPerformed(qualifiedInstance, "update gitops subscription", errSub)
 		}
 	} else {
-		logOnce("The gitops subscription is not owned by us, leaving untouched")
+		// Historically the subscription was owned by the pattern, not the operator. If this is the case,
+		// we update the owner reference to the operator itself.
+		if err := controllerutil.RemoveOwnerReference(qualifiedInstance, sub, r.Scheme); err == nil {
+			if err := controllerutil.SetOwnerReference(operatorConfigMap, sub, r.Scheme); err != nil {
+				return r.actionPerformed(qualifiedInstance, "error setting patterns operator owner reference of gitops subscription", err)
+			}
+			// Persist the updated ownerReferences on the Subscription
+			if _, err := r.olmClient.OperatorsV1alpha1().Subscriptions(SubscriptionNamespace).Update(context.Background(), sub, metav1.UpdateOptions{}); err != nil {
+				return r.actionPerformed(qualifiedInstance, "error updating gitops subscription owner references", err)
+			}
+			return r.actionPerformed(qualifiedInstance, "updated patterns operator owner reference of gitops subscription", nil)
+		} else {
+			logOnce("The gitops subscription is not owned by us, leaving untouched")
+		}
 	}
 	logOnce("subscription found")
 
@@ -528,6 +548,16 @@ func (r *PatternReconciler) finalizeObject(instance *api.Pattern) error {
 			return fmt.Errorf("updated application %q for removal", app.Name)
 		}
 
+		if app.Status.Sync.Status == argoapi.SyncStatusCodeOutOfSync {
+			inProgress, err := syncApplicationWithPrune(r.argoClient, app, ns)
+			if err != nil {
+				return err
+			}
+			if inProgress {
+				return fmt.Errorf("sync with prune and force is already in progress for application %q", app.Name)
+			}
+		}
+
 		if haveACMHub(r) {
 			return fmt.Errorf("waiting for removal of that acm hub")
 		}
@@ -604,7 +634,8 @@ func (r *PatternReconciler) onReconcileErrorWithRequeue(p *api.Pattern, reason s
 	}
 	if duration != nil {
 		log.Printf("Requeueing\n")
-		return reconcile.Result{RequeueAfter: *duration}, err
+		// Return nil error when we have a duration to avoid exponential backoff
+		return reconcile.Result{RequeueAfter: *duration}, nil
 	}
 	return reconcile.Result{}, err
 }
diff --git a/internal/controller/utils.go b/internal/controller/utils.go
index 7ad533a10..4b98e8565 100644
--- a/internal/controller/utils.go
+++ b/internal/controller/utils.go
@@ -40,6 +40,7 @@ import (
 	kerrors "k8s.io/apimachinery/pkg/api/errors"
 	metav1 "k8s.io/apimachinery/pkg/apis/meta/v1"
 	"k8s.io/client-go/kubernetes"
+	ctrl "sigs.k8s.io/controller-runtime"
 
 	configv1 "github.com/openshift/api/config/v1"
 )
@@ -404,3 +405,17 @@ func IsCommonSlimmed(patternPath string) bool {
 	}
 	return true
 }
+
+// Gets the configmap for the Patterns Operator. (Used as an owner reference for the operator itself.)
+func GetOperatorConfigmap() (*corev1.ConfigMap, error) {
+	config, err := ctrl.GetConfig()
+	if err != nil {
+		return nil, fmt.Errorf("failed to get config: %s", err)
+	}
+	clientset, err := kubernetes.NewForConfig(config)
+	if err != nil {
+		return nil, fmt.Errorf("failed to call NewForConfig: %s", err)
+	}
+
+	return clientset.CoreV1().ConfigMaps(OperatorNamespace).Get(context.Background(), OperatorConfigMap, metav1.GetOptions{})
+}