diff --git a/fern/scripts/fern-published-branch.py b/fern/scripts/fern-published-branch.py
index a28be833c..9cb93f36f 100644
--- a/fern/scripts/fern-published-branch.py
+++ b/fern/scripts/fern-published-branch.py
@@ -34,6 +34,10 @@
     "site",
 }
 PUBLISH_METADATA_PATH = Path("fern/publish-metadata.json")
+FERN_ROOT_CONFIG_PATHS = [
+    "fern/docs.yml",
+    "fern/fern.config.json",
+]
 FERN_DEVNOTE_SUPPORT_PATHS = [
     "fern/assets",
     "fern/components/Authors.tsx",
@@ -204,6 +208,12 @@ def copy_path(source: Path, target: Path) -> None:
         shutil.copy2(source, target)
 
 
+def copy_required_path(source: Path, target: Path) -> None:
+    if not source.exists():
+        raise PublishedBranchError(f"Missing required source path: {source}")
+    copy_path(source, target)
+
+
 def clear_published_tree(root: Path) -> None:
     root.mkdir(parents=True, exist_ok=True)
     for path in root.iterdir():
@@ -317,6 +327,14 @@ def materialize_version_nav_pages(published_root: Path) -> None:
             nav.write_text("".join(lines))
 
 
+def sync_fern_root_config(source_root: Path, published_root: Path) -> None:
+    preserved_versions_block = normalize_latest_display_name(versions_block(published_root / "fern" / "docs.yml"))
+    for rel_path in FERN_ROOT_CONFIG_PATHS:
+        copy_required_path(source_root / rel_path, published_root / rel_path)
+    restore_versions_block(published_root / "fern" / "docs.yml", preserved_versions_block)
+    validate_redirect_targets(published_root)
+
+
 def sync_source(args: argparse.Namespace) -> int:
     source_root = Path(args.source_root)
     published_root = Path(args.published_root)
@@ -383,6 +401,8 @@ def patch_devnotes(args: argparse.Namespace) -> int:
     if not target_nav.exists():
         raise PublishedBranchError(f"Missing {target_nav}; publish a Fern release snapshot first")
 
+    sync_fern_root_config(source_root, published_root)
+
     for rel_path in FERN_DEVNOTE_SUPPORT_PATHS:
         copy_path(source_root / rel_path, published_root / rel_path)
 
diff --git a/packages/data-designer/tests/docs/test_fern_published_branch.py b/packages/data-designer/tests/docs/test_fern_published_branch.py
new file mode 100644
index 000000000..9fcd88a5b
--- /dev/null
+++ b/packages/data-designer/tests/docs/test_fern_published_branch.py
@@ -0,0 +1,129 @@
+# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+
+from __future__ import annotations
+
+import argparse
+import importlib.util
+from pathlib import Path
+from types import ModuleType
+
+SCRIPT_PATH = Path(__file__).resolve().parents[4] / "fern" / "scripts" / "fern-published-branch.py"
+
+
+def load_script_module() -> ModuleType:
+    spec = importlib.util.spec_from_file_location("fern_published_branch", SCRIPT_PATH)
+    assert spec is not None
+    loader = spec.loader
+    assert loader is not None
+    module = importlib.util.module_from_spec(spec)
+    loader.exec_module(module)
+    return module
+
+
+def write_text(path: Path, text: str) -> None:
+    path.parent.mkdir(parents=True, exist_ok=True)
+    path.write_text(text)
+
+
+def patch_args(source_root: Path, published_root: Path) -> argparse.Namespace:
+    return argparse.Namespace(
+        source_root=source_root,
+        published_root=published_root,
+        metadata_source_repository=None,
+        metadata_source_ref=None,
+        metadata_source_sha=None,
+        metadata_release_tag=None,
+        metadata_published_branch=None,
+    )
+
+
+def test_patch_devnotes_syncs_root_config_and_preserves_published_versions(tmp_path: Path) -> None:
+    module = load_script_module()
+    source_root = tmp_path / "source"
+    published_root = tmp_path / "published"
+
+    write_text(
+        source_root / "fern" / "docs.yml",
+        """instances:
+- url: datadesigner.docs.buildwithfern.com/nemo/datadesigner
+title: Source Fern Docs
+global-theme: nvidia
+navbar-links:
+- type: github
+  value: https://github.com/NVIDIA-NeMo/DataDesigner
+versions:
+- display-name: "Latest"
+  path: versions/latest.yml
+  slug: latest
+redirects:
+  - source: "/nemo/datadesigner/getting-started"
+    destination: "/nemo/datadesigner/getting-started/welcome"
+""",
+    )
+    write_text(source_root / "fern" / "fern.config.json", '{"organization": "nvidia", "version": "5.41.1"}\n')
+    write_text(source_root / "fern" / "assets" / "current-devnote-asset.png", "new asset")
+    write_text(
+        source_root / "fern" / "versions" / "latest.yml",
+        """navigation:
+  - section: Dev Notes
+    contents:
+      - page: New Note
+        path: ./latest/pages/devnotes/posts/new-note.mdx
+  - section: Concepts
+    contents: []
+""",
+    )
+    write_text(source_root / "fern" / "versions" / "latest" / "pages" / "devnotes" / "posts" / "new-note.mdx", "# New")
+
+    write_text(
+        published_root / "fern" / "docs.yml",
+        """instances:
+- url: datadesigner.docs.buildwithfern.com/nemo/datadesigner
+title: Published Fern Docs
+footer: ./components/OldFooter.tsx
+layout:
+  searchbar-placement: header
+versions:
+- display-name: latest
+  path: versions/latest.yml
+  slug: latest
+- display-name: "v0.6.0"
+  path: versions/v0.6.0.yml
+  slug: v0.6.0
+redirects:
+  - source: "/nemo/datadesigner/getting-started"
+    destination: "/nemo/datadesigner/getting-started/welcome"
+""",
+    )
+    write_text(published_root / "fern" / "fern.config.json", '{"organization": "nvidia", "version": "4.106.0"}\n')
+    write_text(published_root / "fern" / "assets" / "published-only-asset.png", "old asset")
+    write_text(
+        published_root / "fern" / "versions" / "latest.yml",
+        """navigation:
+  - section: Dev Notes
+    contents:
+      - page: Old Note
+        path: ./latest/pages/devnotes/posts/old-note.mdx
+  - section: Concepts
+    contents: []
+""",
+    )
+
+    assert module.patch_devnotes(patch_args(source_root, published_root)) == 0
+
+    published_docs = (published_root / "fern" / "docs.yml").read_text()
+    assert "title: Source Fern Docs" in published_docs
+    assert "global-theme: nvidia" in published_docs
+    assert "navbar-links:" in published_docs
+    assert "title: Published Fern Docs" not in published_docs
+    assert "footer: ./components/OldFooter.tsx" not in published_docs
+    assert "searchbar-placement: header" not in published_docs
+    assert '- display-name: "Latest"' in published_docs
+    assert 'display-name: "v0.6.0"' in published_docs
+    assert (published_root / "fern" / "fern.config.json").read_text() == (
+        '{"organization": "nvidia", "version": "5.41.1"}\n'
+    )
+    assert (published_root / "fern" / "assets" / "current-devnote-asset.png").read_text() == "new asset"
+    assert not (published_root / "fern" / "assets" / "published-only-asset.png").exists()
+    assert (published_root / "fern" / "versions" / "latest" / "pages" / "devnotes" / "posts" / "new-note.mdx").exists()