diff --git a/.github/workflows/sync-harness.yml b/.github/workflows/sync-harness.yml
index 5966e68..3cd9876 100644
--- a/.github/workflows/sync-harness.yml
+++ b/.github/workflows/sync-harness.yml
@@ -109,6 +109,7 @@ jobs:
           token: ${{ steps.app-token.outputs.token }}
           path: target
           persist-credentials: false
+          fetch-depth: 0
       - name: 협업 하네스 동기화
         env:
           GH_TOKEN: ${{ steps.app-token.outputs.token }}
@@ -136,8 +137,15 @@ jobs:
           git -C target config user.name "$APP_SLUG[bot]"
           git -C target config user.email "$bot_id+$APP_SLUG[bot]@users.noreply.github.com"
           git -C target remote set-url origin "https://x-access-token:${GH_TOKEN}@github.com/${TARGET_REPOSITORY}.git"
-          if git -C target ls-remote --exit-code --heads origin "$branch" >/dev/null; then
-            git -C target push origin --delete "$branch"
+          if bash source/sync/check-branch.sh target "$branch"; then
+            :
+          else
+            branch_status=$?
+            if [ "$branch_status" -ne 3 ]; then
+              exit "$branch_status"
+            fi
+            npx --prefix source tsx source/sync/write-result.ts --file "$result_file" --repository "$TARGET_REPOSITORY" --status skipped --detail "잔존 $branch 브랜치에 기본 브랜치에 없는 커밋이 있어 보존했어요. 관리자 확인이 필요해요."
+            exit 0
           fi
           git -C target switch -c "$branch"
           sync_paths=(.agent .codex .claude .github docs/collaboration.md .gitattributes AGENTS.md CLAUDE.md)
@@ -185,7 +193,7 @@ jobs:
         with:
           pattern: sync-result-*
           path: results
-          merge-multiple: true
+          merge-multiple: false
       - name: 동기화 결과 요약
         run: |
           mkdir -p results
diff --git a/sync/attributes.ts b/sync/attributes.ts
index 5e18d42..eafe2d6 100644
--- a/sync/attributes.ts
+++ b/sync/attributes.ts
@@ -33,9 +33,14 @@ export function mergeManagedAttributes(existing = "", attributes: string) {
 
   const block = mergeManagedInstructions("", attributes, markers);
   let inserted = false;
+  const isLegacy = (line: string) => legacyHarnessLines.has(line.replace(/\r?\n$/, ""));
   // Retain line endings and whitespace for every line not owned by the harness.
-  const migrated = lines.map((line) => {
-    if (!legacyHarnessLines.has(line.replace(/\r?\n$/, ""))) return line;
+  const migrated = lines.map((line, index) => {
+    // A separator between removed rules must not become a new blank line at EOF.
+    const tail = lines.slice(index + 1);
+    if (inserted && /^\s*$/.test(line) && tail.some(isLegacy)
+      && tail.every((remaining) => isLegacy(remaining) || /^\s*$/.test(remaining))) return "";
+    if (!isLegacy(line)) return line;
     if (inserted) return "";
     inserted = true;
     return block;
diff --git a/sync/check-branch.sh b/sync/check-branch.sh
new file mode 100644
index 0000000..48a581b
--- /dev/null
+++ b/sync/check-branch.sh
@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+target=$1
+branch=$2
+
+# An absent branch is safe; transport/authentication errors must still fail.
+remote_ref=$(git -C "$target" ls-remote --heads origin "refs/heads/$branch")
+if [ -z "$remote_ref" ]; then
+  exit 0
+fi
+
+git -C "$target" fetch --no-tags origin "refs/heads/$branch"
+if git -C "$target" merge-base --is-ancestor FETCH_HEAD HEAD; then
+  # The old sync was merged: a normal push from the base will fast-forward it.
+  exit 0
+else
+  status=$?
+  if [ "$status" -eq 1 ]; then
+    # Preserve unmerged commits. The caller reports an actionable skipped result.
+    exit 3
+  fi
+  exit "$status"
+fi
diff --git a/sync/report.ts b/sync/report.ts
index 84bec98..e724ccb 100644
--- a/sync/report.ts
+++ b/sync/report.ts
@@ -1,4 +1,5 @@
 import { readdir, readFile } from "node:fs/promises";
+import { join } from "node:path";
 import { fileURLToPath } from "node:url";
 
 const statusText = {
@@ -26,6 +27,29 @@ export function renderSyncReport(results) {
   ].join("\n");
 }
 
+export function parseSyncResults(content: string) {
+  try {
+    return [JSON.parse(content)];
+  } catch {
+    // Accept older newline-delimited results without hiding damaged JSON.
+    return content.split(/\r?\n/).filter(line => line.trim()).map(line => JSON.parse(line));
+  }
+}
+
+export async function readSyncResults(directory: string): Promise<any[]> {
+  const files = await readdir(directory, { withFileTypes: true });
+  const results = await Promise.all(files.map(async (file) => {
+    const path = join(directory, file.name);
+    // Keep artifact directories separate: every target uses sync-result.json.
+    if (file.isDirectory()) return readSyncResults(path);
+    if (file.isFile() && file.name.endsWith(".json")) {
+      return parseSyncResults(await readFile(path, "utf8"));
+    }
+    return [];
+  }));
+  return results.flat();
+}
+
 function argument(name) {
   const index = process.argv.indexOf(name);
   return index >= 0 ? process.argv[index + 1] : null;
@@ -35,10 +59,5 @@ if (process.argv[1] === fileURLToPath(import.meta.url)) {
   const resultsDirectory = argument("--results-directory");
   if (!resultsDirectory) throw new Error("사용법: tsx sync/report.ts --results-directory <directory>");
 
-  const files = await readdir(resultsDirectory, { withFileTypes: true });
-  const results = await Promise.all(files
-    .filter((file) => file.isFile() && file.name.endsWith(".json"))
-    .map(async (file) => JSON.parse(await readFile(resultsDirectory + "/" + file.name, "utf8"))));
-
-  console.log(renderSyncReport(results));
+  console.log(renderSyncReport(await readSyncResults(resultsDirectory)));
 }
diff --git a/tests/attributes.test.ts b/tests/attributes.test.ts
index 8da98a7..6330b31 100644
--- a/tests/attributes.test.ts
+++ b/tests/attributes.test.ts
@@ -1,4 +1,5 @@
 import assert from "node:assert/strict";
+import { execFileSync } from "node:child_process";
 import { mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
@@ -19,7 +20,9 @@ const cases = [
   { name: "빈 파일", existing: "", expected: block },
   { name: "LFS 규칙만 있는 파일", existing: aiLfs, expected: aiLfs + block },
   { name: "마지막 개행이 없는 파일", existing: aiLfs.trimEnd(), expected: aiLfs + block },
-  { name: "마커 없는 기존 하네스 파일", existing: source, expected: block + "\n" },
+  { name: "마커 없는 기존 하네스 파일", existing: source, expected: block },
+  { name: "고유 규칙 뒤의 기존 하네스 파일", existing: aiLfs + source, expected: aiLfs + block },
+  { name: "CRLF 기존 하네스 파일", existing: source.replaceAll("\n", "\r\n"), expected: block },
   { name: "innolive-client의 기존 규칙과 두 LFS 규칙", existing: source + clientLfs, expected: block + "\n" + clientLfs },
   { name: "innolive-ai의 기존 규칙과 LFS 규칙", existing: source + aiLfs, expected: block + "\n" + aiLfs },
   {
@@ -67,6 +70,26 @@ for (const { name, existing, expected } of cases) {
   });
 }
 
+test("innolive-server의 기존 속성 변환은 Git 공백 검사 통과 및 커밋 후 멱등성 유지", async (t) => {
+  const targetRoot = await mkdtemp(join(tmpdir(), "harness-attributes-git-"));
+  t.after(() => rm(targetRoot, { recursive: true, force: true }));
+  const git = (...args: string[]) => execFileSync("git", ["-C", targetRoot, ...args], { encoding: "utf8" });
+  git("init", "-b", "main");
+  git("config", "user.name", "test");
+  git("config", "user.email", "test@example.com");
+  await writeFile(join(targetRoot, ".gitattributes"), source);
+  git("add", ".gitattributes");
+  git("commit", "-m", "initial");
+  const options = { sourceRoot: process.cwd(), targetRoot, items: syncItems.filter(item => item.destination === ".gitattributes") };
+  await applyHarnessFiles(options);
+  git("diff", "--check");
+  git("add", ".gitattributes");
+  git("diff", "--cached", "--check");
+  git("commit", "-m", "sync");
+  await applyHarnessFiles(options);
+  assert.equal(git("status", "--porcelain"), "");
+});
+
 test("원본 규칙이 바뀌어도 이전 하네스 규칙을 중복 없이 이전해요", () => {
   const updatedSource = "*.md text eol=lf\n";
   const expected = "# framework-collaboration-harness:start\n*.md text eol=lf\n# framework-collaboration-harness:end\n\n" + aiLfs;
diff --git a/tests/sync-branch.test.ts b/tests/sync-branch.test.ts
new file mode 100644
index 0000000..71e049d
--- /dev/null
+++ b/tests/sync-branch.test.ts
@@ -0,0 +1,87 @@
+import assert from "node:assert/strict";
+import { execFileSync, spawnSync } from "node:child_process";
+import { mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join, resolve } from "node:path";
+import test from "node:test";
+
+const branch = "harness-sync/framework-agent";
+const script = resolve("sync/check-branch.sh");
+
+async function fixture(t) {
+  const root = await mkdtemp(join(tmpdir(), "harness-branch-"));
+  t.after(() => rm(root, { recursive: true, force: true }));
+  const remote = join(root, "remote.git");
+  const target = join(root, "target");
+  const git = (...args: string[]) => execFileSync("git", ["-C", target, ...args], { encoding: "utf8", stdio: ["ignore", "pipe", "pipe"] }).trim();
+  execFileSync("git", ["init", "--bare", "-b", "main", remote]);
+  execFileSync("git", ["clone", remote, target], { stdio: "pipe" });
+  git("config", "user.name", "test");
+  git("config", "user.email", "test@example.com");
+  await writeFile(join(target, "product.txt"), "product\n");
+  git("add", ".");
+  git("commit", "-m", "initial");
+  git("push", "origin", "main");
+  const check = () => spawnSync("bash", [script, target, branch], { encoding: "utf8" });
+  return { root, remote, target, git, check };
+}
+
+test("동기화 브랜치가 없으면 생성하고 일반 push 가능", async (t) => {
+  const { git, check } = await fixture(t);
+  assert.equal(check().status, 0);
+  git("switch", "-c", branch);
+  git("commit", "--allow-empty", "-m", "sync");
+  git("push", "origin", `HEAD:${branch}`);
+  assert.equal(git("rev-parse", `origin/${branch}`), git("rev-parse", "HEAD"));
+});
+
+test("main에 포함된 잔존 브랜치는 삭제 없이 일반 push 및 재실행 가능", async (t) => {
+  const { target, git, check } = await fixture(t);
+  const oldTip = git("rev-parse", "HEAD");
+  git("push", "origin", `HEAD:${branch}`);
+  git("commit", "--allow-empty", "-m", "base advanced");
+  git("push", "origin", "main");
+  // Match the workflow: apply files before checking remote branch ancestry.
+  await writeFile(join(target, ".gitattributes"), "*.md text eol=lf\n");
+  assert.equal(check().status, 0);
+  assert.equal(git("rev-parse", "FETCH_HEAD"), oldTip);
+  assert.equal(await readFile(join(target, ".gitattributes"), "utf8"), "*.md text eol=lf\n");
+  git("switch", "-c", branch);
+  git("add", ".gitattributes");
+  git("commit", "-m", "sync");
+  git("push", "origin", `HEAD:${branch}`);
+  assert.equal(check().status, 0);
+  assert.equal(git("status", "--porcelain"), "");
+  git("merge-base", "--is-ancestor", oldTip, "HEAD");
+});
+
+test("기본 브랜치에 없는 잔존 커밋은 건너뜀 상태로 반환하고 보존", async (t) => {
+  const { git, check } = await fixture(t);
+  git("switch", "-c", branch);
+  git("commit", "--allow-empty", "-m", "unmerged sync");
+  const remoteTip = git("rev-parse", "HEAD");
+  git("push", "origin", `HEAD:${branch}`);
+  git("switch", "main");
+  git("commit", "--allow-empty", "-m", "base advanced");
+  const baseTip = git("rev-parse", "HEAD");
+  assert.equal(check().status, 3);
+  assert.equal(check().status, 3);
+  assert.equal(git("rev-parse", "HEAD"), baseTip);
+  assert.equal(git("ls-remote", "--heads", "origin", `refs/heads/${branch}`).split(/\s/)[0], remoteTip);
+});
+
+test("원격 조회 실패는 브랜치 없음이나 안전한 건너뜀으로 숨기지 않음", async (t) => {
+  const { root, git, check } = await fixture(t);
+  git("remote", "set-url", "origin", join(root, "missing.git"));
+  const result = check();
+  assert.notEqual(result.status, 0);
+  assert.notEqual(result.status, 3);
+});
+
+test("워크플로는 전체 이력으로 잔존 브랜치를 확인하고 삭제·강제 push 없이 결과 기록", async () => {
+  const workflow = await readFile(".github/workflows/sync-harness.yml", "utf8");
+  assert.match(workflow, /path: target\n\s+persist-credentials: false\n\s+fetch-depth: 0/);
+  assert.match(workflow, /bash source\/sync\/check-branch\.sh target "\$branch"/);
+  assert.match(workflow, /--status skipped --detail/);
+  assert.doesNotMatch(workflow, /git[^\n]*push[^\n]*(--delete|--force|\s-f\s)/);
+});
diff --git a/tests/sync-report.test.ts b/tests/sync-report.test.ts
new file mode 100644
index 0000000..a19c32c
--- /dev/null
+++ b/tests/sync-report.test.ts
@@ -0,0 +1,67 @@
+import assert from "node:assert/strict";
+import { execFileSync } from "node:child_process";
+import { mkdir, mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import test from "node:test";
+import { parseSyncResults, readSyncResults, renderSyncReport } from "../sync/report.ts";
+
+const client = { repository: "team-framework/innolive-client", status: "pr_created", detail: "https://github.com/team-framework/innolive-client/pull/793" };
+const ai = { repository: "team-framework/innolive-ai", status: "pr_created", detail: "https://github.com/team-framework/innolive-ai/pull/81" };
+
+async function fixture(t) {
+  const root = await mkdtemp(join(tmpdir(), "harness-report-"));
+  t.after(() => rm(root, { recursive: true, force: true }));
+  return root;
+}
+
+test("동일 파일명의 아티팩트를 분리된 디렉터리에서 모두 보고", async (t) => {
+  const root = await fixture(t);
+  for (const result of [client, ai]) {
+    const directory = join(root, `sync-result-${result.repository.split("/")[1]}`);
+    await mkdir(directory);
+    await writeFile(join(directory, "sync-result.json"), JSON.stringify(result) + "\n");
+  }
+  const results = await readSyncResults(root);
+  assert.equal(results.length, 2);
+  const report = execFileSync(process.execPath, ["--import", "tsx", "sync/report.ts", "--results-directory", root], { encoding: "utf8" });
+  assert.match(report, /innolive-client.*793/);
+  assert.match(report, /innolive-ai.*81/);
+  const workflow = await readFile(".github/workflows/sync-harness.yml", "utf8");
+  assert.match(workflow, /merge-multiple: false/);
+});
+
+test("단일 JSON과 여러 JSON 줄·빈 줄·CRLF를 지원", () => {
+  assert.deepEqual(parseSyncResults(JSON.stringify(client, null, 2)), [client]);
+  assert.deepEqual(parseSyncResults(["", JSON.stringify(client), "", JSON.stringify(ai), ""].join("\r\n")), [client, ai]);
+});
+
+test("기존 평면 결과와 중첩 JSONL 결과를 함께 읽고 다른 파일은 무시", async (t) => {
+  const root = await fixture(t);
+  await writeFile(join(root, "sync-result.json"), JSON.stringify(client));
+  await mkdir(join(root, "nested"));
+  await writeFile(join(root, "nested", "sync-result.json"), JSON.stringify(ai) + "\n" + JSON.stringify({ repository: "server", status: "skipped", detail: "관리자 확인 필요" }) + "\n");
+  await writeFile(join(root, "README.txt"), "not JSON");
+  const results = await readSyncResults(root);
+  assert.equal(results.length, 3);
+  assert.match(renderSyncReport(results), /server.*건너뜀.*관리자 확인 필요/);
+});
+
+test("손상된 JSON 꼬리는 조용히 버리지 않음", () => {
+  assert.throws(() => parseSyncResults(JSON.stringify(ai) + '\nll/793"}\n'), SyntaxError);
+});
+
+test("write-result 재실행은 append 없이 긴 이전 결과를 완전히 덮어씀", async (t) => {
+  const root = await fixture(t);
+  const file = join(root, "nested", "sync-result.json");
+  for (const result of [client, ai]) {
+    execFileSync(process.execPath, ["--import", "tsx", "sync/write-result.ts", "--file", file, "--repository", result.repository, "--status", result.status, "--detail", result.detail]);
+  }
+  assert.equal(await readFile(file, "utf8"), JSON.stringify(ai) + "\n");
+});
+
+test("결과가 없는 디렉터리는 기존 빈 보고서 유지", async (t) => {
+  const results = await readSyncResults(await fixture(t));
+  assert.deepEqual(results, []);
+  assert.match(renderSyncReport(results), /동기화 대상 레포가 없어요/);
+});