I don’t think the plugin works (properly?) for flexible content.
We make heavy use of flexible content, they are called “flexible_content_”. Under those we have ‘content blocks’ that make up the content, but many of those content block fields can be/are empty.
So querying all “flexible_content” resulted in 250.000+ results, however they are almost all classified as Orphans, when they’re not and still being used on many active pages. Barely any resulted in ‘Empty’.
Testing and deleting the orphans resulted in many of the content being deleted (test environment, no problem).
It’s also a multisite but I doubt that is the issue, the plugin successfully identifies the table and prefixes.
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