Parent pages not found with pretty permalinks

Looks like you’ve sorted the site out. I had the same problem recently working on a WordPress site someone else developed.

The issue was they had registered custom post types and taxonomies with WordPress reserved slugs, like year and term for example. Also avoid registering custom post types and taxonomies that conflict with page or post slugs.

For example: creating a page named Portfolio and registering a custom post type portfolio.

register_post_type('portfolio', $args );

This will cause unexpected problems.

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