diff --git a/packages/core/src/agent/tools.ts b/packages/core/src/agent/tools.ts
index cd02211..54a62bf 100644
--- a/packages/core/src/agent/tools.ts
+++ b/packages/core/src/agent/tools.ts
@@ -103,7 +103,7 @@ export function buildWriteTools(kb: KnowledgeBase, filesChanged: Set<string>, tr
     }),
     patch_concept: tool({
       description:
-        "Targeted update of an existing concept: merge frontmatter keys (null deletes a key) and/or replace one top-level '# Section' body section. Prefer this over write_concept for small edits.",
+        "Targeted update of an existing concept: merge frontmatter keys (null deletes a key) and/or replace one heading body section (any level, H1-H6). Prefer this over write_concept for small edits.",
       inputSchema: z.object({
         path: conceptPath,
         frontmatter: z
@@ -115,7 +115,7 @@ export function buildWriteTools(kb: KnowledgeBase, filesChanged: Set<string>, tr
             heading: z
               .string()
               .min(1)
-              .describe("Top-level heading name, e.g. 'Schema'. Must be non-empty — to replace the whole body use replace_body instead."),
+              .describe("Heading name (any level, # through ######), e.g. 'Schema'. Must be non-empty — to replace the whole body use replace_body instead."),
             content: z.string().describe("New content for that section"),
           })
           .optional(),
diff --git a/packages/core/src/okf/bundle.ts b/packages/core/src/okf/bundle.ts
index b4f5e14..e937548 100644
--- a/packages/core/src/okf/bundle.ts
+++ b/packages/core/src/okf/bundle.ts
@@ -123,7 +123,7 @@ export class Bundle {
 
   /**
    * Targeted update: merge frontmatter keys (null deletes a key) and/or
-   * replace the content under one top-level "# Section" heading.
+   * replace the content under one heading (any level) "# Section".
    */
   async patchConcept(
     bundlePath: string,
@@ -246,21 +246,46 @@ export class Bundle {
   }
 }
 
-/** Replace the content under a top-level heading; append the section if absent. */
+/** Replace the content under a heading of any level; append a top-level
+ * section if absent; throw on ambiguous (multiple) matches. */
 export function replaceSection(body: string, heading: string, content: string): string {
   const normalized = heading.replace(/^#+\s*/, "");
   const lines = body.split("\n");
-  const isHeading = (line: string) => /^#\s+/.test(line);
-  const start = lines.findIndex(
-    (line) => isHeading(line) && line.replace(/^#\s+/, "").trim() === normalized
-  );
+  const isHeading = (line: string) => /^#{1,6}\s+/.test(line);
+  const level = (line: string) => line.match(/^#+/)![0].length;
+  // Title without the leading hashes; an optional ATX closing sequence is
+  // stripped only when preceded by whitespace (CommonMark §4.2 — "Goals##"
+  // is the literal title "Goals##").
+  const headingTitle = (line: string) =>
+    line.replace(/^#{1,6}\s+/, "").trim().replace(/\s+#+$/, "");
+  const matches: number[] = [];
+  for (let i = 0; i < lines.length; i++) {
+    if (isHeading(lines[i]) && headingTitle(lines[i]) === normalized) {
+      matches.push(i);
+    }
+  }
+  if (matches.length > 1) {
+    throw new Error(
+      `replace_section: section "${normalized}" found ${matches.length} times — resolve duplicates via replace_body first.`
+    );
+  }
+  const start = matches.length ? matches[0] : -1;
+  if (start !== -1) {
+    // Normalize: strip a leading content line that duplicates the target heading
+    const cLines = content.split("\n");
+    const fi = cLines.findIndex((l) => l.trim().length > 0);
+    if (fi >= 0 && /^#{1,6}\s+/.test(cLines[fi]) && headingTitle(cLines[fi]) === normalized) {
+      content = cLines.slice(fi + 1).join("\n");
+    }
+  }
   if (start === -1) {
     const suffix = body.trim().length > 0 ? "\n\n" : "";
     return `${body.trimEnd()}${suffix}# ${normalized}\n\n${content.trim()}\n`;
   }
+  const matchedLevel = level(lines[start]);
   let end = lines.length;
   for (let i = start + 1; i < lines.length; i++) {
-    if (isHeading(lines[i])) {
+    if (isHeading(lines[i]) && level(lines[i]) <= matchedLevel) {
       end = i;
       break;
     }
diff --git a/packages/core/test/okf.test.ts b/packages/core/test/okf.test.ts
index 670c90d..300fcdd 100644
--- a/packages/core/test/okf.test.ts
+++ b/packages/core/test/okf.test.ts
@@ -150,6 +150,49 @@ describe("patch", () => {
   });
 });
 
+describe("replaceSection (#34)", () => {
+  it("replaces under a ## heading instead of appending a duplicate section", () => {
+    const body = "# Title\n\nIntro.\n\n## Goals\n\nold\n\n## Notes\n\nn1\n";
+    const out = replaceSection(body, "## Goals", "new goals");
+    expect(out).toBe("# Title\n\nIntro.\n\n## Goals\n\nnew goals\n\n## Notes\n\nn1\n");
+  });
+
+  it("replaces the full section, including nested subsections, up to the next same-or-higher heading", () => {
+    const body = "## Goals\n\na\n\n### Detail\n\nd\n\n## Notes\n\nn\n";
+    const out = replaceSection(body, "Goals", "fresh");
+    expect(out).toBe("## Goals\n\nfresh\n\n## Notes\n\nn\n");
+  });
+
+  it("matches headings written with an ATX closing hash sequence", () => {
+    const body = "# Title\n\nintro\n\n## Goals ##\n\nold\n\n## Notes\n\nn\n";
+    const out = replaceSection(body, "## Goals", "new goals");
+    expect(out).toBe("# Title\n\nintro\n\n## Goals ##\n\nnew goals\n\n## Notes\n\nn\n");
+  });
+
+  it("strips a duplicated heading line at the top of the replacement content", () => {
+    const body = "# Title\n\n## Gotchas\n\nold\n";
+    const out = replaceSection(body, "## Gotchas", "## Gotchas\n\n- fresh gotcha");
+    expect(out).toBe("# Title\n\n## Gotchas\n\n- fresh gotcha\n");
+    expect(out.split("\n").filter((l) => l.trim() === "## Gotchas").length).toBe(1);
+  });
+
+  it("strips a duplicated closing-hash heading line at the top of the replacement content", () => {
+    const body = "# Title\n\n## Gotchas ##\n\nold\n";
+    const out = replaceSection(body, "## Gotchas", "## Gotchas ##\n\n- fresh gotcha");
+    expect(out).toBe("# Title\n\n## Gotchas ##\n\n- fresh gotcha\n");
+  });
+
+  it("throws on ambiguous multi-match instead of editing the first hit", () => {
+    const body = "## A\n\nx\n\n## B\n\nx\n\n## A\n\ny\n";
+    expect(() => replaceSection(body, "A", "z")).toThrow(/found 2 times/);
+  });
+
+  it("still appends a top-level section when absent", () => {
+    const out = replaceSection("body only", "Citations", "[1]");
+    expect(out).toBe("body only\n\n# Citations\n\n[1]\n");
+  });
+});
+
 describe("search", () => {
   beforeEach(async () => {
     await kb.writeConcept(