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Update value of a associative array with update_post_meta

This is plain PHP (logic):

foreach ($existing_list as $key => $value)
    if (isset($existing_list[$key][$add_to_ID]))
        $existing_list[$key][$add_to_ID] = $note;

What you did before was not update the sub-element with key 321 for each element but set the sub-element with that particular key for each element—which is in essence: update where already defined, define otherwise.

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