by Ken Task.
"The Moodle is been configured to create automated backups to local disk"
"local disk' could be moodledata/filedir/. In configuration of auto backups, do you see a path?
It's not PHP skills needed, it's mysql queries (2 - one to find information - and one to remove the row of information in mdl_files table) and command line removal of a targeted file carefully.
That, however, dependent upon answering the question about path.
'SoS', Ken