I had a similar problem this morning when I removed a sub-domain. I couldn’t delete the sub-domains directory, I kept getting ‘permission denied’. In my case, the solution was to re-add then remove the sub-domain. This seemed to fix the permissions, allowing me to delete the directory.
However, I still have a sub-directory in ‘logs’, related to the (now removed) sub-domain that I can’t delete, but I can live with that.
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