diff --git a/lightrag/operate.py b/lightrag/operate.py
index 290f19b6..325bea25 100644
--- a/lightrag/operate.py
+++ b/lightrag/operate.py
@@ -1498,8 +1498,6 @@ async def _merge_nodes_then_upsert(
         reverse=True,
     )[0][0]  # Get the entity type with the highest count
 
-    original_nodes_count = len(nodes_data)
-
     new_source_ids = [dp["source_id"] for dp in nodes_data if dp.get("source_id")]
 
     existing_full_source_ids = []
@@ -1584,12 +1582,12 @@ async def _merge_nodes_then_upsert(
 
     # Combine already_description with sorted new sorted descriptions
     description_list = already_description + sorted_descriptions
-    deduplicated_num = original_nodes_count - len(sorted_descriptions)
+    num_fragment = len(description_list)
+    already_fragment = len(already_description)
+    deduplicated_num = already_fragment + len(nodes_data) - num_fragment
     if deduplicated_num > 0:
         dd_message = f"dd:{deduplicated_num}"
 
-    num_fragment = len(description_list)
-    already_fragment = len(already_description)
     if skip_summary_due_to_limit:
         description = (
             already_node.get("description", "(no description)")
@@ -1818,8 +1816,6 @@ async def _merge_edges_then_upsert(
                     )
                 )
 
-    original_edges_count = len(edges_data)
-
     new_source_ids = [dp["source_id"] for dp in edges_data if dp.get("source_id")]
 
     storage_key = make_relation_chunk_key(src_id, tgt_id)
@@ -1911,12 +1907,12 @@ async def _merge_edges_then_upsert(
 
     # Combine already_description with sorted new descriptions
     description_list = already_description + sorted_descriptions
-    deduplicated_num = original_edges_count - len(sorted_descriptions)
-    if deduplicated_num > 0:
-        dd_message = f"dd:{deduplicated_num}"
 
     num_fragment = len(description_list)
     already_fragment = len(already_description)
+    deduplicated_num = already_fragment + len(edges_data) - num_fragment
+    if deduplicated_num > 0:
+        dd_message = f"dd:{deduplicated_num}"
 
     if skip_summary_due_to_limit:
         description = (
@@ -1924,9 +1920,7 @@ async def _merge_edges_then_upsert(
             if already_edge
             else "(no description)"
         )
-        status_message = (
-            f"Skip merge for `{src_id}`~`{tgt_id}`: KEEP limit reached"
-        )
+        status_message = f"Skip merge for `{src_id}`~`{tgt_id}`: KEEP limit reached"
         logger.debug(status_message)
         if pipeline_status is not None and pipeline_status_lock is not None:
             async with pipeline_status_lock: