diff --git a/src/attune_author/__init__.py b/src/attune_author/__init__.py
index d24a684..9f6a084 100644
--- a/src/attune_author/__init__.py
+++ b/src/attune_author/__init__.py
@@ -9,6 +9,8 @@
 
 from attune_author.manifest import Feature, Manifest, load_manifest
 from attune_author.staleness import (
+    EMPTY_SOURCE_SHA256,
+    EmptySourceError,
     StalenessReport,
     check_staleness,
     check_workspace_staleness,
@@ -21,6 +23,8 @@
     "Manifest",
     "load_manifest",
     # Staleness
+    "EMPTY_SOURCE_SHA256",
+    "EmptySourceError",
     "StalenessReport",
     "check_staleness",
     "check_workspace_staleness",
diff --git a/src/attune_author/cli.py b/src/attune_author/cli.py
index 9454a87..f6b7c01 100644
--- a/src/attune_author/cli.py
+++ b/src/attune_author/cli.py
@@ -30,6 +30,7 @@
     ensure_sidecar,
 )
 from attune_author.mcp.path_validation import validate_file_path
+from attune_author.staleness import EmptySourceError
 
 logger = logging.getLogger(__name__)
 
@@ -485,6 +486,12 @@ def _dispatch(args: argparse.Namespace, parser: argparse.ArgumentParser) -> int:
 
     try:
         return handler(args)
+    except EmptySourceError as e:
+        # Deliberate hard stop: source resolved empty — nothing was
+        # written. Exit non-zero so wrappers (pre-commit, CI, release
+        # prep) see the failure instead of a silently degraded regen.
+        print(f"Error: {e}", file=sys.stderr)
+        return 1
     except (FileNotFoundError, ValueError) as e:
         print(f"Error: {e}", file=sys.stderr)
         return 1
diff --git a/src/attune_author/generator.py b/src/attune_author/generator.py
index 002289b..4c81b2f 100644
--- a/src/attune_author/generator.py
+++ b/src/attune_author/generator.py
@@ -29,7 +29,11 @@
     resolve_write_content,
 )
 from attune_author.manifest import Feature, is_safe_feature_name
-from attune_author.staleness import compute_source_hash
+from attune_author.staleness import (
+    EMPTY_SOURCE_SHA256,
+    EmptySourceError,
+    compute_source_hash,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -461,9 +465,46 @@ def prepare_polish_phase(
         raise ValueError(f"Invalid feature name: {feature.name!r}")
 
     source_hash, matched_files = compute_source_hash(feature, root)
+    template_dir = help_path / "templates" / feature.name
+
+    if not matched_files or source_hash == EMPTY_SOURCE_SHA256:
+        # Empty resolved source is fine for scaffolding a brand-new
+        # feature (no templates on disk yet), but must never OVERWRITE
+        # existing content: the 2026-07-05 incident regen ran against a
+        # wrong project root, resolved every glob to nothing, and
+        # rewrote 36 good templates with degraded empty-source output.
+        at_risk = []
+        for depth in target_depths:
+            if depth not in _ALL_TEMPLATE_NAMES:
+                continue
+            if depth in _PROJECT_DOC_NAMES:
+                out = _project_doc_output_path(depth, feature, root)
+            else:
+                out = template_dir / f"{depth}.md"
+            if out.exists():
+                at_risk.append(str(out))
+        detail = (
+            "no files matched its source globs"
+            if not matched_files
+            else f"all {len(matched_files)} matched file(s) resolved to empty/unreadable content"
+        )
+        if at_risk:
+            raise EmptySourceError(
+                f"Refusing to regenerate templates for '{feature.name}': {detail} "
+                f"under project root {root} (globs: {list(feature.files)!r}), "
+                f"but generated output already exists ({', '.join(at_risk)}). "
+                "Overwriting it from empty source would replace good templates "
+                "with degraded content stamped with the empty-string source_hash "
+                "— check that --project-root points at the repo checkout."
+            )
+        logger.warning(
+            "Scaffolding '%s' from empty source (%s under %s); " "no existing templates at risk",
+            feature.name,
+            detail,
+            root,
+        )
     source_info = _extract_source_info(matched_files, root)
 
-    template_dir = help_path / "templates" / feature.name
     template_dir.mkdir(parents=True, exist_ok=True)
 
     env = _build_jinja_env(help_path)
@@ -1315,7 +1356,9 @@ def _string_collection_values(node: ast.expr) -> list[str] | None:
     return out
 
 
-def _extract_module_constant(node: ast.Assign | ast.AnnAssign) -> dict[str, object] | None:
+def _extract_module_constant(
+    node: ast.Assign | ast.AnnAssign,
+) -> dict[str, object] | None:
     """Return a structured record for a module-level string constant.
 
     Recognizes four shapes that users routinely ask about:
@@ -1420,7 +1463,13 @@ def _extract_class_properties(node: ast.ClassDef) -> list[dict[str, str]]:
         if not _has_property_decorator(child):
             continue
         ret = _unparse_annotation(child.returns) if child.returns else ""
-        props.append({"name": child.name, "return_type": ret, "doc": _docstring_first_line(child)})
+        props.append(
+            {
+                "name": child.name,
+                "return_type": ret,
+                "doc": _docstring_first_line(child),
+            }
+        )
     return props
 
 
@@ -1429,7 +1478,10 @@ def _has_property_decorator(node: ast.FunctionDef | ast.AsyncFunctionDef) -> boo
     for dec in node.decorator_list:
         if isinstance(dec, ast.Name) and dec.id == "property":
             return True
-        if isinstance(dec, ast.Attribute) and dec.attr in ("property", "abstractproperty"):
+        if isinstance(dec, ast.Attribute) and dec.attr in (
+            "property",
+            "abstractproperty",
+        ):
             return True
     return False
 
diff --git a/src/attune_author/staleness.py b/src/attune_author/staleness.py
index 94db3f1..6006cc0 100644
--- a/src/attune_author/staleness.py
+++ b/src/attune_author/staleness.py
@@ -22,7 +22,12 @@
 from dataclasses import dataclass, field
 from pathlib import Path
 
-from attune_author.manifest import Feature, FeatureManifest, is_safe_feature_name, load_manifest
+from attune_author.manifest import (
+    Feature,
+    FeatureManifest,
+    is_safe_feature_name,
+    load_manifest,
+)
 
 logger = logging.getLogger(__name__)
 
@@ -39,6 +44,30 @@
     ".git",
 }
 
+#: SHA-256 of zero bytes. Both hash paths (byte-concatenation and
+#: semantic) produce this digest when a feature's globs match nothing,
+#: or when every matched file is unreadable or empty. A generation run
+#: must never stamp this hash into frontmatter — it means the resolved
+#: source content was empty and the polished output would be degraded
+#: (2026-07-05 incident: a bulk regen against a wrong project root
+#: rewrote 36 templates with this hash).
+EMPTY_SOURCE_SHA256 = hashlib.sha256(b"").hexdigest()
+
+
+class EmptySourceError(RuntimeError):
+    """Empty/unreadable resolved source would overwrite existing output.
+
+    Raised by the generation pipeline (before any file is written)
+    when a feature's source globs resolve to no readable content
+    under the given project root AND generated output already exists
+    on disk. Regenerating from empty source silently replaces good
+    templates with degraded content stamped with the empty-string
+    ``source_hash``, so the pipeline refuses instead. The usual cause
+    is a wrong ``--project-root``. Scaffolding a brand-new feature
+    (no templates on disk yet) from empty source stays allowed.
+    """
+
+
 # Regex to parse the HTML comment footer written by attune-author's doc generator:
 # <!-- attune-generated: source_hash=abc123 feature=foo kind=how-to generated_at=2026-04-23 -->
 _DOC_FOOTER_RE = re.compile(
diff --git a/tests/test_empty_source_guard.py b/tests/test_empty_source_guard.py
new file mode 100644
index 0000000..047be2c
--- /dev/null
+++ b/tests/test_empty_source_guard.py
@@ -0,0 +1,209 @@
+"""Regression tests: refuse to overwrite templates from empty source.
+
+2026-07-05 incident: a bulk regen run against a wrong project root
+resolved every feature's globs to zero files, computed
+``source_hash`` of the empty string
+(e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855),
+and rewrote 36 existing templates with drastically degraded content.
+The generation pipeline must fail loudly (before any write) when
+empty-resolved source would overwrite existing output. Scaffolding a
+brand-new feature (nothing on disk yet) from empty source remains
+allowed — see ``test_feature_glob_with_zero_matches`` in
+``test_generator.py``.
+"""
+
+from __future__ import annotations
+
+from pathlib import Path
+
+import pytest
+
+from attune_author import EMPTY_SOURCE_SHA256, EmptySourceError
+from attune_author.generator import generate_feature_templates, prepare_polish_phase
+from attune_author.manifest import Feature
+
+
+@pytest.fixture
+def feature() -> Feature:
+    return Feature(
+        name="auth",
+        description="Authentication and authorization",
+        files=["src/auth/**"],
+        tags=["security"],
+    )
+
+
+GOOD_TEMPLATE = (
+    "---\n"
+    "type: concept\n"
+    "name: auth-concept\n"
+    "feature: auth\n"
+    "depth: concept\n"
+    "generated_at: 2026-06-23T00:00:00+00:00\n"
+    "source_hash: 544951b28662066a703ef7be552af08e83ef52a5186e5ad71ad216119352938b\n"
+    "status: generated\n"
+    "---\n"
+    "\n"
+    "# Real polished content that must not be clobbered\n"
+)
+
+
+def _seed_existing_template(help_dir: Path) -> Path:
+    """Put a healthy generated template on disk for feature 'auth'."""
+    tdir = help_dir / "templates" / "auth"
+    tdir.mkdir(parents=True)
+    concept = tdir / "concept.md"
+    concept.write_text(GOOD_TEMPLATE, encoding="utf-8")
+    return concept
+
+
+class TestEmptySourceOverwriteGuard:
+    """Empty resolved source + existing output on disk → hard refuse."""
+
+    def test_zero_matched_files_refuses_and_preserves_content(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        concept = _seed_existing_template(help_dir)
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+
+        with pytest.raises(EmptySourceError, match="no files matched"):
+            prepare_polish_phase(
+                feature=feature,
+                help_dir=help_dir,
+                project_root=empty_root,
+                overwrite=True,
+            )
+
+        # The guard fires before any write — existing content intact.
+        assert concept.read_text(encoding="utf-8") == GOOD_TEMPLATE
+
+    def test_all_empty_matched_files_refuses(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        # Non-.py so the legacy byte-concatenation path is exercised;
+        # zero bytes total → the empty-string SHA.
+        _seed_existing_template(help_dir)
+        root = tmp_path / "zerobyte"
+        (root / "src" / "auth").mkdir(parents=True)
+        (root / "src" / "auth" / "data.txt").write_bytes(b"")
+
+        with pytest.raises(EmptySourceError, match="empty/unreadable"):
+            prepare_polish_phase(
+                feature=feature,
+                help_dir=help_dir,
+                project_root=root,
+                overwrite=True,
+            )
+
+    def test_generate_feature_templates_propagates(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        _seed_existing_template(help_dir)
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+
+        with pytest.raises(EmptySourceError):
+            generate_feature_templates(
+                feature=feature,
+                help_dir=help_dir,
+                project_root=empty_root,
+                overwrite=True,
+            )
+
+    def test_scaffolding_new_feature_from_empty_source_allowed(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        # No templates on disk → bootstrap scaffold stays permitted.
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+
+        prep = prepare_polish_phase(
+            feature=feature,
+            help_dir=help_dir,
+            project_root=empty_root,
+            overwrite=True,
+        )
+        assert prep.matched_files == []
+        assert prep.pending
+
+    def test_healthy_source_still_generates(
+        self, feature: Feature, help_dir: Path, project_root: Path
+    ) -> None:
+        _seed_existing_template(help_dir)
+        prep = prepare_polish_phase(
+            feature=feature,
+            help_dir=help_dir,
+            project_root=project_root,
+            overwrite=True,
+        )
+        assert prep.matched_files
+        assert prep.source_hash != EMPTY_SOURCE_SHA256
+        assert prep.pending
+
+    def test_unrecognized_depth_name_is_skipped_not_raised(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        # A depth string outside _ALL_TEMPLATE_NAMES must not crash the
+        # at-risk scan — it's silently skipped, not treated as a file
+        # to check for existing output.
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+
+        prep = prepare_polish_phase(
+            feature=feature,
+            help_dir=help_dir,
+            project_root=empty_root,
+            depths=["not-a-real-depth"],
+            overwrite=True,
+        )
+        assert prep.matched_files == []
+
+    def test_project_doc_depth_at_risk_raises(
+        self, feature: Feature, help_dir: Path, tmp_path: Path
+    ) -> None:
+        # Project-doc kinds (how-to/tutorial/cli-reference/architecture)
+        # resolve their at-risk path via _project_doc_output_path, not
+        # template_dir — must be checked too, not just .help/ templates.
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+        how_to = empty_root / "docs" / "how-to" / f"{feature.name}.md"
+        how_to.parent.mkdir(parents=True)
+        how_to.write_text("# Existing how-to doc\n", encoding="utf-8")
+
+        with pytest.raises(EmptySourceError, match="how-to"):
+            prepare_polish_phase(
+                feature=feature,
+                help_dir=help_dir,
+                project_root=empty_root,
+                depths=["how-to"],
+                overwrite=True,
+            )
+
+
+class TestEmptySourceCLI:
+    """The CLI exits non-zero with a clear message — no traceback."""
+
+    def test_generate_against_empty_root_exits_1(
+        self, help_dir: Path, tmp_path: Path, capsys: pytest.CaptureFixture[str]
+    ) -> None:
+        from attune_author.cli import main
+
+        _seed_existing_template(help_dir)
+        empty_root = tmp_path / "emptyroot"
+        empty_root.mkdir()
+
+        exit_code = main(
+            [
+                "generate",
+                "auth",
+                "--help-dir",
+                str(help_dir),
+                "--project-root",
+                str(empty_root),
+                "--overwrite",
+            ]
+        )
+        assert exit_code == 1
+        err = capsys.readouterr().err
+        assert "Refusing to regenerate" in err