diff --git a/api/internal/plugins/utils/utils.go b/api/internal/plugins/utils/utils.go
index 46706627be..ffd10087aa 100644
--- a/api/internal/plugins/utils/utils.go
+++ b/api/internal/plugins/utils/utils.go
@@ -15,6 +15,7 @@ import (
 	"sigs.k8s.io/kustomize/api/konfig"
 	"sigs.k8s.io/kustomize/api/resid"
 	"sigs.k8s.io/kustomize/api/resmap"
+	"sigs.k8s.io/kustomize/api/resource"
 	"sigs.k8s.io/kustomize/api/types"
 	"sigs.k8s.io/yaml"
 )
@@ -147,34 +148,46 @@ func GetResMapWithIDAnnotation(rm resmap.ResMap) (resmap.ResMap, error) {
 // UpdateResMapValues updates the Resource value in the given ResMap
 // with the emitted Resource values in output.
 func UpdateResMapValues(pluginName string, h *resmap.PluginHelpers, output []byte, rm resmap.ResMap) error {
-	outputRM, err := h.ResmapFactory().NewResMapFromBytes(output)
+	resFactory := h.ResmapFactory().RF()
+	resources, err := resFactory.SliceFromBytes(output)
 	if err != nil {
 		return err
 	}
-	for _, r := range outputRM.Resources() {
+	for _, r := range resources {
 		// for each emitted Resource, find the matching Resource in the original ResMap
 		// using its id
 		annotations := r.GetAnnotations()
 		idString, ok := annotations[idAnnotation]
+		// Transformer-generated resource--add to resMap
 		if !ok {
-			return fmt.Errorf("the transformer %s should not remove annotation %s",
-				pluginName, idAnnotation)
+			if err := rm.Append(r); err != nil {
+				return err
+			}
+			continue
 		}
+
 		id := resid.ResId{}
-		err := yaml.Unmarshal([]byte(idString), &id)
+		err = yaml.Unmarshal([]byte(idString), &id)
 		if err != nil {
 			return err
 		}
+
+		// Outdated ID is likely a duplicated resource--add to resMap
+		if !id.Equals(r.CurId()) {
+			removeIDAnnotation(r)
+			if err := rm.Append(r); err != nil {
+				return err
+			}
+			continue
+		}
+
+		// Existing resource--update in resMap
+
 		res, err := rm.GetByCurrentId(id)
 		if err != nil {
 			return fmt.Errorf("unable to find unique match to %s", id.String())
 		}
-		// remove the annotation set by Kustomize to track the resource
-		delete(annotations, idAnnotation)
-		if len(annotations) == 0 {
-			annotations = nil
-		}
-		r.SetAnnotations(annotations)
+		removeIDAnnotation(r)
 
 		// update the resource value with the transformed object
 		res.ResetPrimaryData(r)
@@ -182,6 +195,16 @@ func UpdateResMapValues(pluginName string, h *resmap.PluginHelpers, output []byt
 	return nil
 }
 
+func removeIDAnnotation(r *resource.Resource) {
+	// remove the annotation set by Kustomize to track the resource
+	annotations := r.GetAnnotations()
+	delete(annotations, idAnnotation)
+	if len(annotations) == 0 {
+		annotations = nil
+	}
+	r.SetAnnotations(annotations)
+}
+
 // UpdateResourceOptions updates the generator options for each resource in the
 // given ResMap based on plugin provided annotations.
 func UpdateResourceOptions(rm resmap.ResMap) (resmap.ResMap, error) {
diff --git a/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go b/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
index 36583095c7..4671794910 100644
--- a/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
+++ b/plugin/someteam.example.com/v1/starlarkmixer/StarlarkMixer_test.go
@@ -38,12 +38,24 @@ data:
 kind: ConfigMap
 metadata:
   annotations:
+    config.kubernetes.io/path: configmap_some-cm.yaml
     modified-by: mixer-instance
   name: some-cm
 ---
 apiVersion: v1
+data:
+  foo: bar
+kind: ConfigMap
+metadata:
+  annotations:
+    config.kubernetes.io/path: configmap_some-cm-copy.yaml
+  name: some-cm-copy
+---
+apiVersion: v1
 kind: ConfigMap
 metadata:
+  annotations:
+    config.kubernetes.io/path: configmap_net-new.yaml
   name: net-new
 `)
 }
diff --git a/plugin/someteam.example.com/v1/starlarkmixer/mixer.star b/plugin/someteam.example.com/v1/starlarkmixer/mixer.star
index be6e6d5a62..bf9d7e2a91 100644
--- a/plugin/someteam.example.com/v1/starlarkmixer/mixer.star
+++ b/plugin/someteam.example.com/v1/starlarkmixer/mixer.star
@@ -1,11 +1,27 @@
 def run(r, fc):
+  add = []
+  remove = []
   for resource in r:
     if resource.get("metadata") == None:
       resource["metadata"] = {}
     if resource["metadata"].get("annotations") == None:
       resource["metadata"]["annotations"] = {}
+
+    # Flag for deletion
+    if resource["metadata"]["name"] == "delete-me":
+      remove.append(resource)
+      continue
+
+    # Deep-ish copy the resource
+    cp = dict(resource)
+    cp["metadata"] = dict(cp["metadata"])
+    cp["metadata"]["annotations"] = dict(cp["metadata"]["annotations"])
+    cp["metadata"]["name"] = resource["metadata"]["name"]+"-copy"
+    add.append(cp)
+
     resource["metadata"]["annotations"]["modified-by"] = fc["metadata"]["name"]
 
+  # Add something
   new = {
     "kind": "ConfigMap",
     "apiVersion": "v1",
@@ -13,6 +29,9 @@ def run(r, fc):
       "name": "net-new"
     }
   }
+  r.extend(add)
   r.append(new)
+  for resource in remove:
+    r.remove(resource)
 
 run(ctx.resource_list["items"], ctx.resource_list["functionConfig"])