diff --git a/changes.d/6096.fix.md b/changes.d/6096.fix.md
new file mode 100644
index 00000000000..d70face335f
--- /dev/null
+++ b/changes.d/6096.fix.md
@@ -0,0 +1 @@
+Fixed bug that caused graph arrows to go missing in the GUI when suicide triggers are present.
\ No newline at end of file
diff --git a/cylc/flow/data_store_mgr.py b/cylc/flow/data_store_mgr.py
index 94354880349..d58cb2ac92d 100644
--- a/cylc/flow/data_store_mgr.py
+++ b/cylc/flow/data_store_mgr.py
@@ -1972,10 +1972,12 @@ def prune_pruned_updated_nodes(self):
                     node = tp_added[tp_id]
                 else:
                     continue
-                for j_id in list(node.jobs) + list(tp_updated[tp_id].jobs):
+                update_node = tp_updated.pop(tp_id)
+                for j_id in list(node.jobs) + list(update_node.jobs):
                     if j_id in j_updated:
                         del j_updated[j_id]
-                del tp_updated[tp_id]
+                self.n_window_edges.difference_update(update_node.edges)
+                self.deltas[EDGES].pruned.extend(update_node.edges)
         self.pruned_task_proxies.clear()
 
     def update_family_proxies(self):