diff --git a/src-tauri/src/mcp_tools.rs b/src-tauri/src/mcp_tools.rs
index 6e7bce5..bb48a05 100644
--- a/src-tauri/src/mcp_tools.rs
+++ b/src-tauri/src/mcp_tools.rs
@@ -1125,37 +1125,55 @@ fn backfill_notes_archive(conn: &rusqlite::Connection) -> Result<String, String>
         .filter_map(|r| r.ok())
         .collect();
 
-    let mut by_project: std::collections::BTreeMap<String, Vec<String>> = std::collections::BTreeMap::new();
+    let mut by_project: std::collections::BTreeMap<String, Vec<(i64, String)>> = std::collections::BTreeMap::new();
     for (id, pid, source, content, created_at) in &rows {
         by_project
             .entry(pid.clone())
             .or_default()
-            .push(note_jsonl_line(*id, pid, source, content, created_at));
+            .push((*id, note_jsonl_line(*id, pid, source, content, created_at)));
     }
 
-    let _guard = NOTES_ARCHIVE_LOCK.lock().map_err(|e| e.to_string())?;
+    // 按「解析后的落盘路径」归并——同路径重复登记（mcp-single-server 已知遗留）指向同一文件，
+    // 若按 project_id 逐项目整写会互相覆盖（2026-09-11 真机回填实锤：后写覆盖先写丢 20 条）
+    let mut by_path: std::collections::BTreeMap<std::path::PathBuf, (Vec<String>, Vec<(i64, String)>)> =
+        std::collections::BTreeMap::new();
     let mut report = String::from("## notes 档案回填（全量重建）\n\n");
-    let (mut archived, mut skipped) = (0usize, 0usize);
-    for (pid, lines) in &by_project {
-        match notes_archive_path(conn, pid) {
+    let mut skipped = 0usize;
+    for (pid, entries) in by_project {
+        match notes_archive_path(conn, &pid) {
             Ok(path) => {
-                if let Some(dir) = path.parent() {
-                    std::fs::create_dir_all(dir).map_err(|e| e.to_string())?;
-                }
-                std::fs::write(&path, lines.join("\n") + "\n").map_err(|e| e.to_string())?;
-                report.push_str(&format!("- ✅ {}：{} 条 → {}\n", pid, lines.len(), path.display()));
-                archived += 1;
+                let slot = by_path.entry(path).or_default();
+                slot.0.push(pid);
+                slot.1.extend(entries);
             }
             Err(e) => {
-                report.push_str(&format!("- ⚠️ {}：跳过（{}），{} 条仅存 DB\n", pid, e, lines.len()));
+                report.push_str(&format!("- ⚠️ {}：跳过（{}），{} 条仅存 DB\n", pid, e, entries.len()));
                 skipped += 1;
             }
         }
     }
+
+    let _guard = NOTES_ARCHIVE_LOCK.lock().map_err(|e| e.to_string())?;
+    let mut archived_notes = 0usize;
+    for (path, (pids, mut entries)) in by_path {
+        entries.sort_by_key(|(id, _)| *id);
+        if let Some(dir) = path.parent() {
+            std::fs::create_dir_all(dir).map_err(|e| e.to_string())?;
+        }
+        let lines: Vec<&str> = entries.iter().map(|(_, l)| l.as_str()).collect();
+        std::fs::write(&path, lines.join("\n") + "\n").map_err(|e| e.to_string())?;
+        archived_notes += entries.len();
+        report.push_str(&format!(
+            "- ✅ {}：{} 条 → {}\n",
+            pids.join(" + "),
+            entries.len(),
+            path.display()
+        ));
+    }
     report.push_str(&format!(
-        "\n共 {} 条笔记；{} 个项目已归档，{} 个跳过（跳过项待修复登记路径后重跑即可）。",
+        "\n共 {} 条笔记，{} 条已归档，{} 个项目登记被跳过（修复登记路径后重跑即可）。",
         rows.len(),
-        archived,
+        archived_notes,
         skipped
     ));
     Ok(report)
@@ -1513,6 +1531,36 @@ mod tests {
         assert_eq!(count2, 3, "重跑不应翻倍");
     }
 
+    #[test]
+    fn notes_backfill_merges_duplicate_registrations_same_path() {
+        // 同路径重复登记（mcp-single-server 已知遗留）：两条 project 记录指向同一目录，
+        // 回填必须归并写入而非互相覆盖（2026-09-11 真机实锤丢 20 条的回归）
+        let conn = rusqlite::Connection::open_in_memory().unwrap();
+        setup_notes_schema(&conn);
+        let base = temp_base("duppath");
+        for pid in ["uuid-form", "name-form"] {
+            conn.execute(
+                "INSERT INTO project_workspaces (id, win_path) VALUES (?1, ?2)",
+                rusqlite::params![pid, base.to_str().unwrap()],
+            )
+            .unwrap();
+        }
+        for i in 0..3 {
+            conn.execute(
+                "INSERT INTO project_notes (project_id, content) VALUES ('uuid-form', ?1)",
+                [format!("a-{i}")],
+            )
+            .unwrap();
+        }
+        conn.execute("INSERT INTO project_notes (project_id, content) VALUES ('name-form', 'b-0')", []).unwrap();
+
+        let report = backfill_notes_archive(&conn).expect("回填应成功");
+        let file = base.join(".blueprint").join("notes-archive.jsonl");
+        let text = std::fs::read_to_string(&file).unwrap();
+        assert_eq!(text.lines().count(), 4, "同路径两登记的笔记应全部归并: {report}");
+        assert!(report.contains("4 条已归档"), "报告应按笔记数计数: {report}");
+    }
+
     #[test]
     fn notes_archive_concurrent_appends_no_interleave() {
         let base = temp_base("concurrent");