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WPSSO Core should comment the JSON it detects (and uses) in the content, but between the time it detects the JSON (adding it to the Schema markup in the head section) and the time it can comment it, if the JSON has changed (been optimized or reformatted, for example), then it will not be able to comment it as the original JSON it detected is no longer there. If the JSON in the content does not change, it should be commented automatically.
If you prefer the FAQ markup to be disconnected from the @graph markup created by WPSSO Core, you can disable the hasPart property using this filter in your functions.php file:
add_filter( 'wpsso_init_json_filter_prop_haspart', '__return_false' );Note that you must be using at least WPSSO Core v15 for this to work.
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