Description of problem:
In some situation original file doesn't get restored while they are available in /usr/etc/.

How reproducible:
Reproducible when try to modify a file available in /usr/etc/ and /etc/ but not owned by any rpm.

Steps to Reproduce:

1. Install a 4.6 or older version cluster (also observed on 4.3). Get shell access into one of the worker node. Notice that /etc/iscsi/initiatorname.iscsi and /usr/etc/initiatorname.iscsi both exist but not owned by any rpm package.

$ rpm -qf /etc/iscsi/initiatorname.iscsi 
file /etc/iscsi/initiatorname.iscsi is not owned by any package

2. Create following Machinconfig

$ cat iscsi-mc.yaml 
apiVersion: machineconfiguration.openshift.io/v1
kind: MachineConfig
metadata:
  labels:
    machineconfiguration.openshift.io/role: worker
  name: 99-iscsi-initiator
spec:
  config:
    ignition:
      version: 2.2.0
    storage:
      files:
        - contents:
            source: data:text/plain;charset=utf-8;base64,SW5pdGlhdG9yTmFtZT1pcW4uMTk5NC0wNS5jb20ubnV0YW5peDprOHMtd29ya2VyCg==
          filesystem: root
          mode: 420
          path: /etc/iscsi/initiatorname.iscsi

2. Apply the Machinconfig by running `oc create -f iscsi-mc.yaml`
3. MachineConfig is successfully applied on worker node, can be verified by getting access to one of worker node and check content of /etc/iscsi/initiatorname.iscsi
3. Now delete the applied MachineConfig by running `oc delete mc 99-iscsi-initiator`
4. Observe the MCD log and will see in the log
"Deleting stale config file: /etc/iscsi/initiatorname.iscsi"

Expected results:
/etc/iscsi/initiatorname.iscsi gets restored with file content available in /usr/etc/iscsi/initiatorname.iscsi