diff --git a/scripts/generate.py b/scripts/generate.py
index e8f1f1b..05c3f63 100644
--- a/scripts/generate.py
+++ b/scripts/generate.py
@@ -51,6 +51,8 @@ def main(src_top, dest_top):
     docs = load_all(src_top)
     files_generated = 0
 
+    doc_to_headline_remapping = {}
+
     os.makedirs(dest_top, exist_ok=True)
     graph = {}
     for doc in docs:
@@ -87,29 +89,36 @@ def main(src_top, dest_top):
             # print("Skip:", relpath)
             continue
 
-        if doc.id is not None:
-            topHeadlines = doc.getTopHeadlines()
+        main_headline = None
+        topHeadlines = doc.getTopHeadlines()
 
-            if ((len(topHeadlines) == 1 and related is None)
-                or (len(topHeadlines) == 2 and related is not None)):
+        if ((len(topHeadlines) == 1 and related is None)
+            or (len(topHeadlines) == 2 and related is not None)):
+
+            main_headline = [h for h in topHeadlines if h != related][0]
+            if doc.id is not None:
                 endpath = os.path.join(dest_top, doc.id + ".node.html")
-
-                main_headline = [h for h in topHeadlines if h != related][0]
                 with open(endpath, "wt") as f:
+                    doc_to_headline_remapping['id:' + doc.id] = 'id:' + main_headline.id
+
                     f.write(as_document(render(main_headline, doc, headlineLevel=0)))
                     files_generated += 1
-            else:
-                logging.error("Cannot render document from id: {}. {} headlines {} related".format(
-                    relpath,
-                    len(topHeadlines),
-                    'with' if related is not None else 'without'
-                ))
+        elif doc.id is not None:
+            logging.error("Cannot render document from id: {}. {} headlines {} related".format(
+                relpath,
+                len(topHeadlines),
+                'with' if related is not None else 'without'
+            ))
 
         for headline in headlines:
             endpath = os.path.join(dest_top, headline.id + ".node.html")
 
             links = []
-            for l in headline.get_links():
+            headline_links = list(headline.get_links())
+            if headline == main_headline and related is not None:
+                headline_links.extend(list(related.get_links()))
+
+            for l in headline_links:
                 if l.value.startswith('http://') or l.value.startswith('https://'):
                     pass # Ignore for now, external URL
                 elif l.value.startswith('id:'):
@@ -147,6 +156,13 @@ def main(src_top, dest_top):
                 f.write(as_document(render(headline, doc, headlineLevel=0)))
                 files_generated += 1
 
+    # Update graph, replace document ids with headline ids
+    for headline_data in graph.values():
+        for link in headline_data['links']:
+            if link['target'] in doc_to_headline_remapping:
+                link['target'] = doc_to_headline_remapping[link['target']]
+
+    # Output graph files
     graphpath = os.path.join(dest_top, "graph.json")
     graph_explorer_path = os.path.join(dest_top, "graph.html")
     with open(graphpath, "wt") as f: