diff --git a/pkg/sync/sync_context.go b/pkg/sync/sync_context.go
index 38fc8747b..477517c28 100644
--- a/pkg/sync/sync_context.go
+++ b/pkg/sync/sync_context.go
@@ -5,7 +5,6 @@ import (
 	"encoding/json"
 	"fmt"
 	"sort"
-	"strconv"
 	"strings"
 	"sync"
 	"time"
@@ -781,21 +780,11 @@ func (sc *syncContext) getSyncTasks() (_ syncTasks, successful bool) {
 	    endWave := uniquePruneWaves[n-1-i]
 	
 	    for _, task := range pruneTasks[startWave] {
-			annotations := task.liveObj.GetAnnotations()
-			if annotations == nil {
-				annotations = make(map[string]string)
-			}
-			annotations[common.AnnotationSyncWave] = strconv.Itoa(endWave)
-			task.liveObj.SetAnnotations(annotations)
+			task.waveOverride = &endWave
 	    }
 	
 	    for _, task := range pruneTasks[endWave] {
-			annotations := task.liveObj.GetAnnotations()
-			if annotations == nil {
-				annotations = make(map[string]string)
-			}
-			annotations[common.AnnotationSyncWave] = strconv.Itoa(startWave)
-			task.liveObj.SetAnnotations(annotations)
+			task.waveOverride = &startWave
 	    }
 	}
 
@@ -814,12 +803,7 @@ func (sc *syncContext) getSyncTasks() (_ syncTasks, successful bool) {
 	for _, task := range tasks {
 		if task.isPrune() &&
 			(sc.pruneLast || resourceutil.HasAnnotationOption(task.liveObj, common.AnnotationSyncOptions, common.SyncOptionPruneLast)) {
-			annotations := task.liveObj.GetAnnotations()
-			if annotations == nil {
-				annotations = make(map[string]string)
-			}
-			annotations[common.AnnotationSyncWave] = strconv.Itoa(syncPhaseLastWave)
-			task.liveObj.SetAnnotations(annotations)
+			task.waveOverride = &syncPhaseLastWave
 		}
 	}
 
diff --git a/pkg/sync/sync_context_test.go b/pkg/sync/sync_context_test.go
index 83c0ad7b8..2e2740609 100644
--- a/pkg/sync/sync_context_test.go
+++ b/pkg/sync/sync_context_test.go
@@ -1911,31 +1911,48 @@ func TestWaitForCleanUpBeforeNextWave(t *testing.T) {
 	pod1.SetName("pod-1")
 	pod2 := NewPod()
 	pod2.SetName("pod-2")
+	pod3 := NewPod()
+	pod3.SetName("pod-3")
 
 	pod1.SetAnnotations(map[string]string{synccommon.AnnotationSyncWave: "1"})
 	pod2.SetAnnotations(map[string]string{synccommon.AnnotationSyncWave: "2"})
+	pod3.SetAnnotations(map[string]string{synccommon.AnnotationSyncWave: "3"})
 
 	syncCtx := newTestSyncCtx(nil)
 	syncCtx.prune = true
 
-	// prune order : pod2 -> pod1
+	// prune order : pod3 -> pod2 -> pod1
 	syncCtx.resources = groupResources(ReconciliationResult{
-		Target: []*unstructured.Unstructured{nil, nil},
-		Live:   []*unstructured.Unstructured{pod1, pod2},
+		Target: []*unstructured.Unstructured{nil, nil, nil},
+		Live:   []*unstructured.Unstructured{pod1, pod2, pod3},
 	})
 
 	var phase common.OperationPhase
 	var msg string
 	var result []common.ResourceSyncResult
 
-	// 1st sync should prune only pod2
+	// 1st sync should prune only pod3
 	syncCtx.Sync()
 	phase, _, result = syncCtx.GetState()
 	assert.Equal(t, synccommon.OperationRunning, phase)
 	assert.Equal(t, 1, len(result))
-	assert.Equal(t, "pod-2", result[0].ResourceKey.Name)
+	assert.Equal(t, "pod-3", result[0].ResourceKey.Name)
 	assert.Equal(t, synccommon.ResultCodePruned, result[0].Status)
 
+	// simulate successful delete of pod3
+	syncCtx.resources = groupResources(ReconciliationResult{
+		Target: []*unstructured.Unstructured{nil, nil, },
+		Live:   []*unstructured.Unstructured{pod1, pod2, },
+	})
+
+	// next sync should prune only pod2
+	syncCtx.Sync()
+	phase, _, result = syncCtx.GetState()
+	assert.Equal(t, synccommon.OperationRunning, phase)
+	assert.Equal(t, 2, len(result))
+	assert.Equal(t, "pod-2", result[1].ResourceKey.Name)
+	assert.Equal(t, synccommon.ResultCodePruned, result[1].Status)
+
 	// add delete timestamp on pod2 to simulate pending delete
 	pod2.SetDeletionTimestamp(&metav1.Time{Time: time.Now()})
 
@@ -1945,11 +1962,9 @@ func TestWaitForCleanUpBeforeNextWave(t *testing.T) {
 	phase, msg, result = syncCtx.GetState()
 	assert.Equal(t, synccommon.OperationRunning, phase)
 	assert.Equal(t, "waiting for deletion of /Pod/pod-2", msg)
-	assert.Equal(t, 1, len(result))
+	assert.Equal(t, 2, len(result))
 
 	// simulate successful delete of pod2
-	pod2.SetDeletionTimestamp(nil)
-	pod2 = nil
 	syncCtx.resources = groupResources(ReconciliationResult{
 		Target: []*unstructured.Unstructured{nil, },
 		Live:   []*unstructured.Unstructured{pod1, },
@@ -1960,10 +1975,12 @@ func TestWaitForCleanUpBeforeNextWave(t *testing.T) {
 	syncCtx.Sync()
 	phase, _, result = syncCtx.GetState()
 	assert.Equal(t, synccommon.OperationSucceeded, phase)
-	assert.Equal(t, 2, len(result))
-	assert.Equal(t, "pod-2", result[0].ResourceKey.Name)
-	assert.Equal(t, "pod-1", result[1].ResourceKey.Name)
+	assert.Equal(t, 3, len(result))
+	assert.Equal(t, "pod-3", result[0].ResourceKey.Name)
+	assert.Equal(t, "pod-2", result[1].ResourceKey.Name)
+	assert.Equal(t, "pod-1", result[2].ResourceKey.Name)
 	assert.Equal(t, synccommon.ResultCodePruned, result[0].Status)
 	assert.Equal(t, synccommon.ResultCodePruned, result[1].Status)
+	assert.Equal(t, synccommon.ResultCodePruned, result[2].Status)
 
 }