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The settings file is a general file that would apply this protection to all the organization's repositories. If there are repositories that do not have that branch name, you have to reset it to empty in the specific repo file (I don't know if it would also work in the suborg file) and add a new element with the protection configuration of that branch to that specific repository. This will cause the general branch to be deleted from the configuration and only the branch of that repository to be added. This is because by default what the configuration does is add all the configurations that exist.
I remember a similar question and it was explained how to do it. I don't know if it is already in the documentation or it was left as a comment in some issue.
branch policies have issue if you .github/settings doesn't have the same branch as repo.yml
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