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There are a few calls to switch_to_blog() in intuitive-custom-post-order.php, but no calls to restore_current_blog(), which causes ms_is_switched() to always be true. Yoast for example, checks ms_is_switched() before saving values to the database. As it always returns true, the yoast data is never saved.
https://wordpress.org/support/topic/bug-leads-to-incompatibility-with-yoast-seo-in-multisite/