diff --git a/graphify/affected.py b/graphify/affected.py
index bd70b276..dbb532b4 100644
--- a/graphify/affected.py
+++ b/graphify/affected.py
@@ -210,7 +210,13 @@ def load_graph(path: Path) -> nx.Graph:
     import json
     from networkx.readwrite import json_graph
 
-    raw = json.loads(path.read_text(encoding="utf-8"))
+    try:
+        raw = json.loads(path.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError) as exc:
+        raise RuntimeError(
+            f"Cannot read graph file {path}: {exc}. "
+            "Re-run 'graphify extract' to regenerate it."
+        ) from exc
     # Force directed so stored caller→callee direction survives the round-trip;
     # mirrors serve.py and __main__.py (#1174).
     raw = {**raw, "directed": True}
diff --git a/graphify/build.py b/graphify/build.py
index 2de02b2a..6fcf241b 100644
--- a/graphify/build.py
+++ b/graphify/build.py
@@ -746,7 +746,13 @@ def build_merge(
         # NetworkX round-trip loses direction permanently (#760).
         from graphify.security import check_graph_file_size_cap
         check_graph_file_size_cap(graph_path)
-        data = json.loads(graph_path.read_text(encoding="utf-8"))
+        try:
+            data = json.loads(graph_path.read_text(encoding="utf-8"))
+        except (json.JSONDecodeError, OSError) as exc:
+            raise RuntimeError(
+                f"Cannot read {graph_path} for incremental merge: {exc}. "
+                "Delete the file and run a full rebuild."
+            ) from exc
         links_key = "links" if "links" in data else "edges"
         existing_nodes = list(data.get("nodes", []))
         existing_edges = list(data.get(links_key, []))
diff --git a/graphify/diagnostics.py b/graphify/diagnostics.py
index 4d8abe29..ff66fa95 100644
--- a/graphify/diagnostics.py
+++ b/graphify/diagnostics.py
@@ -274,7 +274,13 @@ def _read_json_file(path: str | Path) -> dict[str, Any]:
 
     json_path = Path(path)
     check_graph_file_size_cap(json_path)
-    data = json.loads(json_path.read_text(encoding="utf-8"))
+    try:
+        data = json.loads(json_path.read_text(encoding="utf-8"))
+    except (json.JSONDecodeError, OSError) as exc:
+        raise RuntimeError(
+            f"Cannot parse {json_path}: {exc}. "
+            "The file may be corrupted — re-run 'graphify extract'."
+        ) from exc
     if not isinstance(data, dict):
         raise ValueError("diagnostic input must be a JSON object")
     return data