kubernetes: Validation error on kubectl apply after kubectl edit

What happened: Attempting to kubectl apply a manifest whose resources have been previously modified using kubectl edit (see steps to reproduce below) raises a validation error.

kubectl apply -f manifest.yml 
configmap/example unchanged
The Deployment "example" is invalid: spec.template.spec.containers[0].env[0].valueFrom: Invalid value: "": may not be specified when `value` is not empty

What you expected to happen: Manifest should be successfully applied.

If this flow is not supported, the user should receive a useful error message indicating what the problem is (e.g. “Resource has been modified since last applied configuration, cannot update”).

How to reproduce it (as minimally and precisely as possible):

1. Create manifest.yml with the following contents:

---
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
  name: example
  namespace: default
spec:
  replicas: 1
  selector:
    matchLabels:
      cluster: example
  template:
    metadata:
      labels:
        cluster: example
    spec:
      containers:
      - command: [ sleep, '3600' ]
        env:
        - name: EXAMPLE
          valueFrom:
            configMapKeyRef:
              name: example
              key: example
        image: alpine
        name: sleep

---
apiVersion: v1
data:
  example: value
kind: ConfigMap
metadata:
  name: example
  namespace: default

1. Apply manifest kubectl apply -f manifest.yml

2. Edit the example deployment to change the environment variable to point to a value instead of a configmap key. kubectl edit deployment example

        - name: EXAMPLE
          value: 'example'

1. Repeat step 2. kubectl apply -f manifest.yml

Anything else we need to know?:

Environment:

• Kubernetes version (use kubectl version):

Client Version: version.Info{Major:"1", Minor:"14", GitVersion:"v1.14.2", GitCommit:"66049e3b21efe110454d67df4fa62b08ea79a19b", GitTreeState:"clean", BuildDate:"2019-05-16T16:23:09Z", GoVersion:"go1.12.5", Compiler:"gc", Platform:"linux/amd64"}
Server Version: version.Info{Major:"1", Minor:"10", GitVersion:"v1.10.7", GitCommit:"0c38c362511b20a098d7cd855f1314dad92c2780", GitTreeState:"clean", BuildDate:"2018-08-20T09:56:31Z", GoVersion:"go1.9.3", Compiler:"gc", Platform:"linux/amd64"}

• Cloud provider or hardware configuration: AWS
• OS (e.g: cat /etc/os-release): Debian GNU/Linux 9 (stretch)
• Kernel (e.g. uname -a):

Linux ip-10-110-247-162 4.9.0-7-amd64 #1 SMP Debian 4.9.110-3+deb9u2 (2018-08-13) x86_64 GNU/Linux

• Install tools: kops
• Network plugin and version (if this is a network-related bug): N/A
• Others: N/A