It’s all going into the same table, you’re possibly not using the correct key name to insert it. The only thing that differentiates custom field keys and keys used for metaboxes is that metabox keys are typically prefixed with an underscore to hide them from the list that shows up in the custom fields section. it’s also possible to store multiple things as an array under a single entry. that may be the case if you’re using a metabox helper class of some sort to generate the metaboxes. look directly in the table to see how your metabox data is being stored.
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