diff --git a/graphify/build.py b/graphify/build.py
index 579d7a35..f180419d 100644
--- a/graphify/build.py
+++ b/graphify/build.py
@@ -337,18 +337,21 @@ def build_merge(
 
     # Prune nodes and edges from deleted source files
     if prune_sources:
-        prune_set = set(prune_sources)
-        # Manifest stores absolute paths; graph nodes store relative paths.
-        # Add relative variants so both formats match regardless of OS or
-        # whether paths were relativized at build time (#1007).
-        if root is not None:
-            import os as _os
-            _root = Path(root)
-            for p in list(prune_sources):
-                try:
-                    prune_set.add(str(Path(p).relative_to(_root)).replace(_os.sep, "/"))
-                except ValueError:
-                    pass
+        # Build a set containing both the raw form (matches nodes that kept
+        # absolute source_file) and the normalised relative form (matches nodes
+        # that were relativised by _norm_source_file at build time).
+        # .resolve() handles symlinked roots and redundant ".." / "./" segments
+        # so Path.relative_to() succeeds even when the scan root is a symlink.
+        # (#1007: manifest absolute paths vs graph relative source_file mismatch)
+        _root_str = str(Path(root).resolve()) if root is not None else None
+        prune_set: set[str] = set()
+        for p in prune_sources:
+            if not p:
+                continue
+            prune_set.add(p)
+            norm = _norm_source_file(p, _root_str)
+            if norm:
+                prune_set.add(norm)
         to_remove = [
             n for n, d in G.nodes(data=True)
             if d.get("source_file") in prune_set
diff --git a/tests/test_build.py b/tests/test_build.py
index 7552aa6a..065d7f41 100644
--- a/tests/test_build.py
+++ b/tests/test_build.py
@@ -348,9 +348,8 @@ def test_build_from_json_relative_source_file_unchanged(tmp_path):
 
 def test_build_merge_prune_absolute_paths_match_relative_nodes(tmp_path):
     """#1007: manifest stores absolute paths, graph nodes store relative paths.
-    prune_sources with absolute paths must still remove the right nodes."""
-    import json
-    from graphify.export import to_json
+    prune_sources with absolute paths must still remove the right nodes and edges."""
+    import networkx as nx
 
     root = tmp_path / "corpus"
     root.mkdir()
@@ -360,20 +359,44 @@ def test_build_merge_prune_absolute_paths_match_relative_nodes(tmp_path):
     chunk = {"nodes": [
         {"id": "n1", "label": "login", "file_type": "code", "source_file": "module_a/auth.py"},
         {"id": "n2", "label": "format_date", "file_type": "code", "source_file": "module_b/utils.py"},
-    ], "edges": []}
+    ], "edges": [
+        {"source": "n1", "target": "n2", "relation": "calls", "confidence": "EXTRACTED",
+         "source_file": "module_b/utils.py", "weight": 1.0},
+    ]}
     G0 = build([chunk], dedup=False)
-    import networkx as nx
-    graph_path.write_text(
-        json.dumps(nx.node_link_data(G0, edges="edges")), encoding="utf-8"
-    )
+    graph_path.write_text(json.dumps(nx.node_link_data(G0, edges="edges")), encoding="utf-8")
 
-    # prune_sources from manifest — absolute paths
+    # prune_sources from manifest — absolute paths (what detect_incremental emits)
     deleted_abs = [str(root / "module_b" / "utils.py")]
     G1 = build_merge([], graph_path, prune_sources=deleted_abs, dedup=False, root=root)
 
     node_labels = {d["label"] for _, d in G1.nodes(data=True)}
     assert "format_date" not in node_labels, "stale node from deleted file should be pruned"
     assert "login" in node_labels, "unrelated node must survive"
+    # Edge from deleted file must also be gone
+    assert G1.number_of_edges() == 0, "edge from deleted source_file should be pruned"
+
+
+def test_build_merge_prune_windows_backslash_paths(tmp_path):
+    """#1007: prune_sources with Windows-style backslash absolute paths must still match."""
+    import networkx as nx
+
+    root = tmp_path / "corpus"
+    root.mkdir()
+    graph_path = tmp_path / "graph.json"
+
+    chunk = {"nodes": [
+        {"id": "n1", "label": "parse_date", "file_type": "code", "source_file": "module_b/utils.py"},
+    ], "edges": []}
+    G0 = build([chunk], dedup=False)
+    graph_path.write_text(json.dumps(nx.node_link_data(G0, edges="edges")), encoding="utf-8")
+
+    # Simulate Windows manifest path with backslashes
+    win_path = str(root / "module_b" / "utils.py").replace("/", "\\")
+    G1 = build_merge([], graph_path, prune_sources=[win_path], dedup=False, root=root)
+
+    node_labels = {d["label"] for _, d in G1.nodes(data=True)}
+    assert "parse_date" not in node_labels, "node should be pruned even with backslash path"
 
 
 def test_build_merge_rejects_oversized_existing_graph(monkeypatch, tmp_path):