can not delete files without everything breaking

## Problem Description
if you delete or rename a file eg. a suborg or repository file, safesettings stops being able to apply anything untill you add the file back.

### What is actually happening
delete a file eg. under suborgs -> third-party.yml
open a PR and the validitor will produce an empty validator comment
merge and the safe settings run on the commit does not show up at all
open a new PR with a change, validator shows the change
merge and safe settings run on the commit throws an error
(specific error depends on the change before but it always errors and stops once you add the file, even if empty back)

### What is the expected behavior
I can delete old suborg or repo files and this will be detected and just set what is in the org level settings and not break all safe settings runs from then on.

## Context

### running our own

### github.com

#### sha of SS bult 861d70f1d24427f523363a83709429d7aa041510