I think the method you're looking for is whereHas (under the heading "Querying Relationship Existence").
$questions = \App\ContentLegacy::with('staff', 'meta', 'questionStandards')
->where('post_type','nm_question')
->whereHas('meta', function ($query) {
$query->where('meta_key', 'flagged');
})
->orderBy("post_date", "DES")
->paginate(20);
The has method can take a callback argument too, but in this case that would be more verbose.
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