diff --git a/src/application/HermesConfigurationYaml.ts b/src/application/HermesConfigurationYaml.ts
index 8d245da37..61eb0dfde 100644
--- a/src/application/HermesConfigurationYaml.ts
+++ b/src/application/HermesConfigurationYaml.ts
@@ -1,7 +1,7 @@
 import {
   isScalar,
-  parse,
   parseDocument,
+  type Document,
   type ParsedNode,
   type ScalarTag,
   type Tags,
@@ -56,9 +56,28 @@ const HERMES_YAML_OPTIONS = {
       a.source === b.source),
 };
 
-/** Parse a Hermes `config.yaml`. */
-export const parseHermesConfigurationYaml = (text: string): unknown =>
-  parse(text, HERMES_YAML_OPTIONS);
+// A comment-only document has no root; a bare marker has an unwritten null
+// scalar. Explicit null values, tags and anchors remain actual values.
+const isEmptyYamlRoot = (root: Document["contents"]): boolean =>
+  root === null ||
+  (isScalar(root) &&
+    root.value === null &&
+    root.source === "" &&
+    root.tag === undefined &&
+    root.anchor === undefined);
+
+const parseHermesDocument = (text: string) => {
+  const document = parseDocument(text, HERMES_YAML_OPTIONS);
+  const error = document.errors[0];
+  if (error !== undefined) throw error;
+  return document;
+};
+
+/** Parse a Hermes `config.yaml`, preserving the distinction between no root and explicit null. */
+export const parseHermesConfigurationYaml = (text: string): unknown => {
+  const document = parseHermesDocument(text);
+  return isEmptyYamlRoot(document.contents) ? {} : document.toJS();
+};
 
 /** Set or delete one value in a Hermes `config.yaml`, keeping the rest as written. */
 export const editHermesConfigurationYaml = (
@@ -66,7 +85,16 @@ export const editHermesConfigurationYaml = (
   path: readonly string[],
   value: unknown,
 ): string => {
-  const document = parseDocument(text, HERMES_YAML_OPTIONS);
+  // A plain Document, so a bare `---` root can be replaced by a new map.
+  const document: Document = parseHermesDocument(text);
+  const root = document.contents;
+  if (isScalar(root) && isEmptyYamlRoot(root)) {
+    const map = document.createNode({});
+    map.commentBefore = [root.commentBefore, root.comment]
+      .filter((comment) => comment !== undefined)
+      .join("\n");
+    document.contents = map;
+  }
   if (value === undefined) document.deleteIn(path);
   else document.setIn(path, value);
   // Editing REA must not reflow unrelated user prompts or other YAML scalars.
diff --git a/tests/boundary/filesystem/hermesClientConfiguration.test.ts b/tests/boundary/filesystem/hermesClientConfiguration.test.ts
index 218573d5c..7bd72a676 100644
--- a/tests/boundary/filesystem/hermesClientConfiguration.test.ts
+++ b/tests/boundary/filesystem/hermesClientConfiguration.test.ts
@@ -114,18 +114,34 @@ describe("Hermes YAML shape diagnostics", () => {
       "!!omap [{rea: {command: rea, args: [mcp]}}]",
       "!!timestamp 2001-12-15",
       "!!binary cmVh",
-    ].flatMap((value) => [
-      {
-        original: `${value}\n`,
-        problem: "The configuration root must be an object",
-      },
-      {
-        original: `mcp_servers: ${value}\n`,
-        problem: '"mcp_servers" must be an object',
-      },
-    ]),
+    ]
+      .flatMap((value) => [
+        {
+          original: `${value}\n`,
+          problem: "The configuration root must be an object",
+        },
+        {
+          original: `mcp_servers: ${value}\n`,
+          problem: '"mcp_servers" must be an object',
+        },
+      ])
+      .concat(
+        // An explicit null root is a value, not an empty file.
+        [
+          "null\n",
+          "~\n",
+          "# Hermes configuration\nnull\n",
+          "--- ~\n",
+          "--- !!null\n",
+          '!!null ""\n',
+          "--- &empty\n",
+        ].map((original) => ({
+          original,
+          problem: "The configuration root must be an object",
+        })),
+      ),
   )(
-    "blocks setup and uninstall before changes for tagged non-record YAML: $original",
+    "blocks setup and uninstall before changes for tagged or null non-record YAML: $original",
     async ({ original, problem }) => {
       const { home, client } = await hermesClient();
       const cursor = join(home, ".cursor", "mcp.json");
@@ -281,7 +297,36 @@ mcp_servers:
     });
   });
 
-  it.each(["", "\n"])(
+  // Comments and a bare document marker parse to a null document, like an
+  // empty file, and are kept ahead of the new registration.
+});
+
+describe("Hermes YAML empty configurations", () => {
+  it("rejects multiple YAML documents before treating an empty first root as absent", async () => {
+    const { client } = await hermesClient();
+    const original =
+      "---\n---\nmcp_servers:\n  rea:\n    command: rea\n    args: [mcp]\n";
+    await writeFile(client.configPath, original);
+    expect(await inspectClientConfiguration(client, {}, command)).toMatchObject(
+      { status: "invalid" },
+    );
+    expect(await configureClientConfiguration(client, {}, command)).toEqual({
+      status: "failed",
+      reason: "readback",
+    });
+    expect(await readFile(client.configPath, "utf8")).toBe(original);
+    await expect(
+      readFile(`${client.configPath}.rea.backup`, "utf8"),
+    ).rejects.toThrow();
+  });
+
+  it.each([
+    "",
+    "\n",
+    "# Hermes configuration\n",
+    "---\n",
+    "---\n# Hermes configuration\n",
+  ])(
     "configures an empty config.yaml %j as a new document",
     async (original) => {
       const { home, client } = await hermesClient();
@@ -289,7 +334,10 @@ mcp_servers:
       expect(
         (await configureClientConfiguration(client, {}, command)).status,
       ).toBe("configured");
-      expect(parseYaml(await readFile(client.configPath, "utf8"))).toEqual({
+      const text = await readFile(client.configPath, "utf8");
+      const kept = original.trimEnd();
+      expect(text.slice(0, kept.length)).toBe(kept);
+      expect(parseYaml(text)).toEqual({
         mcp_servers: {
           rea: { command: command[0], args: command.slice(1), enabled: true },
         },