diff --git a/.changeset/fix-apply-symlink-conflict.md b/.changeset/fix-apply-symlink-conflict.md
new file mode 100644
index 0000000..366dfbf
--- /dev/null
+++ b/.changeset/fix-apply-symlink-conflict.md
@@ -0,0 +1,5 @@
+---
+"@stainless-code/codemap": patch
+---
+
+Reject apply targets that are symlinks so phase-2 rename cannot replace a link with a regular file.
diff --git a/src/application/apply-engine.test.ts b/src/application/apply-engine.test.ts
index 758d9b9..0091a14 100644
--- a/src/application/apply-engine.test.ts
+++ b/src/application/apply-engine.test.ts
@@ -1,10 +1,12 @@
 import { describe, expect, it } from "bun:test";
 import {
   chmodSync,
+  lstatSync,
   mkdirSync,
   mkdtempSync,
   readFileSync,
   readdirSync,
+  symlinkSync,
   writeFileSync,
 } from "node:fs";
 import { tmpdir } from "node:os";
@@ -597,6 +599,38 @@ describe("applyDiffPayload", () => {
 
       expect(result.conflicts[0]?.reason).toBe("path escapes project root");
     });
+
+    it("rejects symlinked file_path and leaves the symlink intact", () => {
+      const root = tmpProject();
+      writeSource(root, "real.ts", "const foo = 1;\n");
+      symlinkSync(join(root, "real.ts"), join(root, "link.ts"));
+
+      const result = applyDiffPayload({
+        rows: [
+          {
+            file_path: "link.ts",
+            line_start: 1,
+            before_pattern: "foo",
+            after_pattern: "bar",
+          },
+        ],
+        projectRoot: root,
+        dryRun: false,
+      });
+
+      expect(result.applied).toBe(false);
+      expect(result.conflicts).toEqual([
+        {
+          file_path: "link.ts",
+          line_start: 1,
+          before_pattern: "foo",
+          actual_at_line: "",
+          reason: "path is a symlink",
+        },
+      ]);
+      expect(lstatSync(join(root, "link.ts")).isSymbolicLink()).toBe(true);
+      expect(readSource(root, "real.ts")).toBe("const foo = 1;\n");
+    });
   });
 
   describe("overlap detection (F2 — triangulated review 2026-05-06)", () => {
diff --git a/src/application/apply-engine.ts b/src/application/apply-engine.ts
index b0dde9b..1794038 100644
--- a/src/application/apply-engine.ts
+++ b/src/application/apply-engine.ts
@@ -30,7 +30,7 @@
  */
 
 import { randomBytes } from "node:crypto";
-import { readFileSync, renameSync, writeFileSync } from "node:fs";
+import { lstatSync, readFileSync, renameSync, writeFileSync } from "node:fs";
 import { isAbsolute, resolve } from "node:path";
 
 import {
@@ -82,6 +82,7 @@ export type ConflictReason =
   | "line out of range"
   | "line content drifted"
   | "path escapes project root"
+  | "path is a symlink"
   | "duplicate edit on same line";
 
 /** Q5 envelope shape — single shape across `dry-run` and `apply` modes. */
@@ -172,8 +173,23 @@ export function applyDiffPayload(opts: ApplyDiffPayloadOpts): ApplyJsonPayload {
 
     let source = sourceCache.get(canonicalPath);
     if (source === undefined) {
+      const absPath = resolve(resolvedRoot, canonicalPath);
       try {
-        source = readFileSync(resolve(resolvedRoot, canonicalPath), "utf8");
+        if (lstatSync(absPath).isSymbolicLink()) {
+          conflicts.push({
+            file_path: canonicalPath,
+            line_start: lineStart,
+            before_pattern: before,
+            actual_at_line: "",
+            reason: "path is a symlink",
+          });
+          continue;
+        }
+      } catch {
+        // Missing path — readFileSync below reports "file missing".
+      }
+      try {
+        source = readFileSync(absPath, "utf8");
       } catch {
         conflicts.push({
           file_path: canonicalPath,