Edit Deployment Directly

$ kubectl -n flux-system edit deployment helm-controller

Export and Update

$ kubectl -n flux-system get deployment helm-controller -o yaml > helm-controller.yaml
$ vi helm-controller.yaml 
$ kubectl apply -f helm-controller.yaml

Patch a Deployment

Patch:

spec:
  template:
    spec:
      securityContext:
        runAsUser: 999

$ kubectl -n flux-system patch deployment notification-controller --patch "$(cat patch.yaml)"