So I did update the manifest and replaced apiVersion: extensions/v1beta1 to apiVersion: apps/v1

apiVersion: apps/v1
kind: Deployment
metadata:
  name: secretmanager
  namespace: kube-system
spec:
  selector:
    matchLabels:
      app: secretmanager
  template:
    metadata:
      labels:
        app: secretmanager
    spec:
    ...

I then applied the change

k apply -f deployment.yaml

Warning: kubectl apply should be used on resource created by either kubectl create --save-config or kubectl apply
deployment.apps/secretmanager configured

I also tried

k replace --force -f deployment.yaml

That recreated the POD (downtime :( ) but still if you try to output the yaml config of the deployment I see the old value

k get deployments -n kube-system secretmanager -o yaml 

apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  annotations:
    deployment.kubernetes.io/revision: "1"
    kubectl.kubernetes.io/last-applied-configuration: |
      {"apiVersion":"apps/v1","kind":"Deployment",
      "metadata":{"annotations":{},"name":"secretmanager","namespace":"kube-system"}....}
  creationTimestamp: "2020-08-21T21:43:21Z"
  generation: 2
  name: secretmanager
  namespace: kube-system
  resourceVersion: "99352965"
  selfLink: /apis/extensions/v1beta1/namespaces/kube-system/deployments/secretmanager
  uid: 3d49aeb5-08a0-47c8-aac8-78da98d4c342
spec:

So I still see this apiVersion: extensions/v1beta1

What I am doing wrong?

I am preparing eks kubernetes v1.15 to be migrated over to v1.16