diff --git a/src/domain/native/codeSigningPosture.ts b/src/domain/native/codeSigningPosture.ts
index e678d924a9..72003f901a 100644
--- a/src/domain/native/codeSigningPosture.ts
+++ b/src/domain/native/codeSigningPosture.ts
@@ -45,7 +45,7 @@ export const sealedResourcesSchema = z.object({
 /** Local `codesign --verify --deep --strict` outcome for the signed code. */
 export const signatureVerificationSchema = z.object({
   path: z.string(),
-  status: z.enum(["valid", "invalid", "unsigned"]),
+  status: z.enum(["valid", "invalid", "unsigned", "unknown"]),
   exit_code: z.number().int().nullable(),
   diagnostics: z.array(z.string()),
   validated_nested_code: z.array(z.string()),
diff --git a/src/native/NativeMacOSProvider.ts b/src/native/NativeMacOSProvider.ts
index 763cba07b1..51ba729f50 100644
--- a/src/native/NativeMacOSProvider.ts
+++ b/src/native/NativeMacOSProvider.ts
@@ -422,21 +422,15 @@ class NativeMacOSClient implements AnalysisClient {
       unsigned,
     );
     limitations.push(...(await unconfirmedNestedCode(verification)));
-    if (
-      verification.status === "invalid" &&
-      verification.diagnostics.some((line) =>
-        /permission denied|operation not permitted|\bEACCES\b|\bEPERM\b/iu.test(
-          line,
-        ),
-      )
-    )
+    if (verification.status === "unknown")
       limitations.push(
-        "Signature verification reported a permission or I/O diagnostic; the invalid status may reflect unreadable nested code rather than a broken signature.",
+        "Signature verification could not read its target (permission or I/O diagnostic); the unknown status reflects an operational failure, not a proven broken signature.",
       );
     // Deep verification covers nested code: when it fails only there, the
     // main executable's own signature may still be valid. Check it directly
     // before hiding its facets as unauthenticated.
-    let mainInvalid = verification.status === "invalid";
+    let mainInvalid =
+      verification.status === "invalid" || verification.status === "unknown";
     if (mainInvalid && !unsigned && verifyPath !== this.target.path) {
       const mainVerify = await this.#verifySignature(this.target.path, signal);
       if (!mainVerify.ok) return mainVerify;
diff --git a/src/native/NativeSignaturePosture.ts b/src/native/NativeSignaturePosture.ts
index 5ca7e792c5..e768ec3231 100644
--- a/src/native/NativeSignaturePosture.ts
+++ b/src/native/NativeSignaturePosture.ts
@@ -54,26 +54,43 @@ const bundleDirFromPlist = (plist: string): string | undefined => {
  * `--prepared:`/`--validated:` progress lines arrive in no fixed order; they
  * are reported as a sorted list of validated nested code instead.
  */
+/** Diagnostics showing verification could not read its target. */
+export const verificationIOFailure = (
+  diagnostics: readonly string[],
+): boolean =>
+  diagnostics.some((line) =>
+    /permission denied|operation not permitted|\bEACCES\b|\bEPERM\b/iu.test(
+      line,
+    ),
+  );
+
 export const signatureVerification = (
   capture: NativeCommandCapture,
   path: string,
   unsigned: boolean,
 ): NonNullable<InspectSignature["verification"]> => {
-  // Preserve trailing whitespace: a nested path may end in a space or tab.
-  // Strip only the line delimiter and leading whitespace for record parsing.
+  // Preserve trailing whitespace and carriage returns: a nested path may end
+  // in a space, tab, or CR. codesign delimits records with LF, so split on LF
+  // only and strip leading whitespace for record parsing.
   const lines = `${capture.stderr}\n${capture.stdout}`
-    .split(/\r?\n/u)
-    .map((line) => line.replace(/\r$/u, ""))
+    .split(/\n/u)
     .filter((line) => line.length > 0);
   const record = (line: string): string => line.replace(/^\s+/u, "");
+  const diagnostics = lines.filter(
+    (line) => !/^--(?:prepared|validated):/u.test(record(line)),
+  );
   return {
     path,
     status:
-      capture.exitCode === 0 ? "valid" : unsigned ? "unsigned" : "invalid",
+      capture.exitCode === 0
+        ? "valid"
+        : unsigned
+          ? "unsigned"
+          : verificationIOFailure(diagnostics)
+            ? "unknown"
+            : "invalid",
     exit_code: capture.exitCode,
-    diagnostics: lines.filter(
-      (line) => !/^--(?:prepared|validated):/u.test(record(line)),
-    ),
+    diagnostics,
     validated_nested_code: [
       ...new Set(
         lines.flatMap((line) => {
@@ -156,6 +173,28 @@ export const stapledTicket = async (
           size: null,
           reason: "changed",
         };
+      // An atomic replacement swaps the pathname to a new inode while the
+      // handle still describes the unlinked original: re-resolve the path and
+      // refuse a digest that no longer belongs to the bundle.
+      try {
+        const current = await lstat(path);
+        if (current.dev !== opened.dev || current.ino !== opened.ino)
+          return {
+            status: "unreadable",
+            path: relative,
+            sha256: null,
+            size: null,
+            reason: "changed",
+          };
+      } catch {
+        return {
+          status: "unreadable",
+          path: relative,
+          sha256: null,
+          size: null,
+          reason: "changed",
+        };
+      }
       return {
         status: "present",
         path: relative,
diff --git a/tests/boundary/providers/native/nativeSignaturePosture.test.ts b/tests/boundary/providers/native/nativeSignaturePosture.test.ts
index 05018240a4..5779c2b520 100644
--- a/tests/boundary/providers/native/nativeSignaturePosture.test.ts
+++ b/tests/boundary/providers/native/nativeSignaturePosture.test.ts
@@ -330,7 +330,27 @@ describe("native signature posture slice-aware cases", () => {
     );
   });
 
-  it("flags permission diagnostics separately from invalid signatures", async () => {
+  it("preserves a trailing carriage return in reported nested paths", async () => {
+    const { app, executable } = await fixtureApp(undefined);
+    const signature = await new NativeMacOSProvider(
+      new CarriageReturnPathRunner(),
+      "darwin",
+    )
+      .createClient(machoTarget(executable, app))
+      .execute("inspect_signature", {});
+    if (!signature.ok) throw signature.error;
+    const result = inspectSignatureSchema.parse(signature.value.result);
+    // The CR is a valid pathname byte, not a line delimiter: it is kept and
+    // the nonexistent path is flagged rather than silently normalized.
+    expect(result.verification?.validated_nested_code).toEqual([
+      `${app}/Contents/Helpers/cr\r`,
+    ]);
+    expect(result.limitations).toContainEqual(
+      expect.stringContaining("which does not exist"),
+    );
+  });
+
+  it("reports verification I/O failures as unknown, not invalid", async () => {
     const { app, executable } = await fixtureApp(undefined);
     const signature = await new NativeMacOSProvider(
       new PermissionDeniedRunner(),
@@ -340,9 +360,11 @@ describe("native signature posture slice-aware cases", () => {
       .execute("inspect_signature", {});
     if (!signature.ok) throw signature.error;
     const result = inspectSignatureSchema.parse(signature.value.result);
-    expect(result.verification?.status).toBe("invalid");
+    expect(result.verification?.status).toBe("unknown");
     expect(result.limitations).toContainEqual(
-      expect.stringContaining("permission or I/O diagnostic"),
+      expect.stringContaining(
+        "operational failure, not a proven broken signature",
+      ),
     );
   });
 });
@@ -459,6 +481,23 @@ class UniversalMixedRunner extends FixtureRunner {
   }
 }
 
+/** A nested helper whose file name ends in a carriage return. */
+class CarriageReturnPathRunner extends FixtureRunner {
+  override async run(tool: string, arguments_: readonly string[]) {
+    const result = await super.run(tool, arguments_);
+    if (!result.ok || arguments_[0] !== "--verify") return result;
+    const bundle = arguments_.at(-1) ?? "";
+    const stderr = `--validated:${bundle}/Contents/Helpers/cr\r\n${bundle}: valid on disk\n`;
+    return ok({
+      ...result.value,
+      stdout: "",
+      stderr,
+      stdoutBytes: 0,
+      stderrBytes: Buffer.byteLength(stderr),
+    });
+  }
+}
+
 /** Verification fails because nested code cannot be read. */
 class PermissionDeniedRunner extends FixtureRunner {
   override async run(tool: string, arguments_: readonly string[]) {