diff --git a/scripts/lib/ghidra-checkpoint-refusal.d.mts b/scripts/lib/ghidra-checkpoint-refusal.d.mts
new file mode 100644
index 0000000000..9762e1aa2e
--- /dev/null
+++ b/scripts/lib/ghidra-checkpoint-refusal.d.mts
@@ -0,0 +1,12 @@
+/** Require the CLI's explicit refusal instead of accepting an unrelated failure. */
+export function requireCheckpointCliRefusal(
+  operation: () => Promise<unknown>,
+  expectedCode: string,
+): Promise<{ readonly code: string; readonly [key: string]: unknown }>;
+
+/** Verify refusal before the caller restores its deliberately invalid manifest. */
+export function assertCheckpointRefusalPreservesManifest(
+  operation: () => Promise<unknown>,
+  manifestPath: string,
+  expectedBytes: Uint8Array,
+): Promise<{ readonly code: string; readonly [key: string]: unknown }>;
diff --git a/scripts/lib/ghidra-checkpoint-refusal.mjs b/scripts/lib/ghidra-checkpoint-refusal.mjs
new file mode 100644
index 0000000000..85a5a59fa8
--- /dev/null
+++ b/scripts/lib/ghidra-checkpoint-refusal.mjs
@@ -0,0 +1,33 @@
+import assert from "node:assert/strict";
+import { readFile } from "node:fs/promises";
+
+/** Require the CLI's explicit refusal instead of accepting an unrelated failure. */
+export async function requireCheckpointCliRefusal(operation, expectedCode) {
+  let refusal;
+  try {
+    await operation();
+  } catch (cause) {
+    assert.equal(cause.code, 1, cause.stderr);
+    refusal = JSON.parse(cause.stdout);
+  }
+  assert.ok(refusal, "CLI unexpectedly accepted unavailable checkpoint state");
+  assert.equal(refusal.code, expectedCode, JSON.stringify(refusal));
+  return refusal;
+}
+
+/** Verify refusal before the caller restores its deliberately invalid manifest. */
+export async function assertCheckpointRefusalPreservesManifest(
+  operation,
+  manifestPath,
+  expectedBytes,
+) {
+  const refusal = await requireCheckpointCliRefusal(
+    operation,
+    "configuration_invalid",
+  );
+  assert.ok(
+    (await readFile(manifestPath)).equals(expectedBytes),
+    `Refused CLI command changed the checkpoint manifest: ${manifestPath}`,
+  );
+  return refusal;
+}
diff --git a/scripts/lib/real-ghidra-boundaries.mjs b/scripts/lib/real-ghidra-boundaries.mjs
index 1e5d97c23c..ebdb475d0a 100644
--- a/scripts/lib/real-ghidra-boundaries.mjs
+++ b/scripts/lib/real-ghidra-boundaries.mjs
@@ -212,7 +212,12 @@ export async function verifyGhidraBoundaries(
   );
   const names = await call("list_names");
   const batchIdentity = await verifyGhidraBatchIdentity(call, names);
-  const instructionFlow = await verifyGhidraInstructionFlow(call, names, cli);
+  const instructionFlow = await verifyGhidraInstructionFlow(
+    call,
+    names,
+    cli,
+    target,
+  );
   const leaf = names.find((item) =>
     item.value.endsWith("rea_ghidra_inventory_leaf"),
   );
diff --git a/scripts/lib/real-ghidra-instruction-flow.d.mts b/scripts/lib/real-ghidra-instruction-flow.d.mts
new file mode 100644
index 0000000000..70abf8964e
--- /dev/null
+++ b/scripts/lib/real-ghidra-instruction-flow.d.mts
@@ -0,0 +1,19 @@
+import type { BinaryTarget } from "../../src/domain/binaryTargetTypes.js";
+
+/** Check source-owned inventory controls using independently parsed target facts. */
+export function verifyGhidraInstructionFlow(
+  call: (
+    operation: string,
+    parameters: Readonly<Record<string, string>>,
+  ) => Promise<unknown>,
+  names: readonly { readonly address: string; readonly value: string }[],
+  cli: (command: string, address: string) => Promise<unknown>,
+  target: Pick<BinaryTarget, "format" | "architecture"> | null,
+): Promise<{
+  readonly return_instruction: string;
+  readonly decoded_pcode_return: true;
+  readonly return_cli_mcp_parity: true;
+  readonly explicit_x86_elf_controls: number;
+  readonly explicit_control_scope: string;
+  readonly generic_unknown_preserved: true;
+}>;
diff --git a/scripts/lib/real-ghidra-instruction-flow.mjs b/scripts/lib/real-ghidra-instruction-flow.mjs
index 25bad8073e..bafbc13b2f 100644
--- a/scripts/lib/real-ghidra-instruction-flow.mjs
+++ b/scripts/lib/real-ghidra-instruction-flow.mjs
@@ -1,7 +1,13 @@
 import assert from "node:assert/strict";
 
 /** Verify decoded return evidence and distinct non-return flows on owned fixtures. */
-export async function verifyGhidraInstructionFlow(call, names, cli) {
+export async function verifyGhidraInstructionFlow(call, names, cli, target) {
+  // inventory.c emits these controls only for an x86-64 ELF compilation.
+  // Provider name omission cannot establish whether that source branch applied.
+  const controlsRequired =
+    target !== null &&
+    target.format === "elf" &&
+    target.architecture === "x86_64";
   const leaf = names.find((item) =>
     item.value.endsWith("rea_ghidra_inventory_leaf"),
   );
@@ -31,6 +37,11 @@ export async function verifyGhidraInstructionFlow(call, names, cli) {
   let checked = 0;
   for (const [symbol, mnemonic, bytes] of controls) {
     const procedure = names.find((item) => item.value === symbol);
+    if (controlsRequired)
+      assert.ok(
+        procedure,
+        `Source fixture lacks expected decoder control ${symbol}`,
+      );
     if (procedure === undefined) continue;
     const before = await call("resolve_containing_procedure", {
       address: procedure.address,
@@ -72,9 +83,11 @@ export async function verifyGhidraInstructionFlow(call, names, cli) {
     return_cli_mcp_parity: true,
     explicit_x86_elf_controls: checked,
     explicit_control_scope:
-      checked === 0
-        ? "Not present on this host-native fixture format/architecture"
-        : "x86-64 ELF",
+      target === null
+        ? "Unknown: source fixture format/architecture was not established"
+        : controlsRequired
+          ? "x86-64 ELF"
+          : "Not compiled for this fixture format/architecture",
     generic_unknown_preserved: true,
   };
 }
diff --git a/scripts/verify-real-ghidra-checkpoints.mjs b/scripts/verify-real-ghidra-checkpoints.mjs
index 3b5788fce4..540c870d22 100644
--- a/scripts/verify-real-ghidra-checkpoints.mjs
+++ b/scripts/verify-real-ghidra-checkpoints.mjs
@@ -24,6 +24,10 @@ import {
   requireMcpOperationResult,
   requireMcpToolError,
 } from "./lib/mcp-verifier-results.mjs";
+import {
+  requireCheckpointCliRefusal,
+  assertCheckpointRefusalPreservesManifest,
+} from "./lib/ghidra-checkpoint-refusal.mjs";
 import {
   createVerifierRun,
   completeVerifierRun,
@@ -109,18 +113,6 @@ async function cli(procedure, flags = [], path = target) {
   );
   return JSON.parse(stdout);
 }
-async function refuseCli(procedure, flags, expected) {
-  let refusal;
-  try {
-    await cli(procedure, flags);
-  } catch (cause) {
-    assert.equal(cause.code, 1, cause.stderr);
-    refusal = JSON.parse(cause.stdout);
-  }
-  assert.ok(refusal, "CLI unexpectedly accepted unavailable checkpoint state");
-  assert.equal(refusal.code, expected, JSON.stringify(refusal));
-  return refusal;
-}
 async function connect(environment = {}) {
   const owner = createVerifierMcpOwner();
   const client = new Client({
@@ -346,9 +338,8 @@ int main(void) { CheckpointRecord record = { 3, 11 }; return rea_checkpoint_leaf
   await phase(
     "an older immutable REA snapshot refuses the changed checkpoint",
     async () => {
-      const refusal = await refuseCli(
-        "rea_checkpoint_leaf",
-        ["--snapshot", snapshotPath],
+      const refusal = await requireCheckpointCliRefusal(
+        () => cli("rea_checkpoint_leaf", ["--snapshot", snapshotPath]),
         "evidence_integrity_mismatch",
       );
       assert.ok(refusal.details.binding_mismatch.profile_digest);
@@ -390,12 +381,16 @@ int main(void) { CheckpointRecord record = { 3, 11 }; return rea_checkpoint_leaf
   await phase(
     "target/profile mismatch is refused without replacing the saved state",
     async () => {
+      const attemptedBytes = Buffer.from(
+        JSON.stringify({ ...current, target_sha256: "0".repeat(64) }),
+      );
       try {
-        await writeFile(
+        await writeFile(manifestPath, attemptedBytes);
+        await assertCheckpointRefusalPreservesManifest(
+          () => cli("rea_checkpoint_retained"),
           manifestPath,
-          JSON.stringify({ ...current, target_sha256: "0".repeat(64) }),
+          attemptedBytes,
         );
-        await refuseCli("rea_checkpoint_retained", [], "configuration_invalid");
       } finally {
         await writeFile(manifestPath, bytes);
       }
@@ -405,9 +400,14 @@ int main(void) { CheckpointRecord record = { 3, 11 }; return rea_checkpoint_leaf
   await phase(
     "malformed manifest is refused without a fresh import",
     async () => {
+      const attemptedBytes = Buffer.from("{");
       try {
-        await writeFile(manifestPath, "{");
-        await refuseCli("rea_checkpoint_retained", [], "configuration_invalid");
+        await writeFile(manifestPath, attemptedBytes);
+        await assertCheckpointRefusalPreservesManifest(
+          () => cli("rea_checkpoint_retained"),
+          manifestPath,
+          attemptedBytes,
+        );
       } finally {
         await writeFile(manifestPath, bytes);
       }
@@ -426,7 +426,10 @@ int main(void) { CheckpointRecord record = { 3, 11 }; return rea_checkpoint_leaf
       await copyFile(packed, backup);
       try {
         await writeFile(packed, "corrupted packed data");
-        await refuseCli("rea_checkpoint_retained", [], "configuration_invalid");
+        await requireCheckpointCliRefusal(
+          () => cli("rea_checkpoint_retained"),
+          "configuration_invalid",
+        );
       } finally {
         await copyFile(backup, packed);
       }
diff --git a/tests/conformance/providers/ghidra/checkpointRefusal.test.ts b/tests/conformance/providers/ghidra/checkpointRefusal.test.ts
new file mode 100644
index 0000000000..05efc6abf2
--- /dev/null
+++ b/tests/conformance/providers/ghidra/checkpointRefusal.test.ts
@@ -0,0 +1,78 @@
+import { mkdtemp, readFile, rm, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { expect, it, onTestFinished } from "vitest";
+import { assertCheckpointRefusalPreservesManifest } from "../../../../scripts/lib/ghidra-checkpoint-refusal.mjs";
+
+const checkpointFile = async (bytes: Uint8Array) => {
+  const root = await mkdtemp(join(tmpdir(), "rea-checkpoint-refusal-"));
+  onTestFinished(() => rm(root, { recursive: true, force: true }));
+  const path = join(root, "current.json");
+  await writeFile(path, bytes);
+  return path;
+};
+
+const refusal = (code = "configuration_invalid", exitCode = 1) =>
+  Object.assign(new Error("inert CLI refusal"), {
+    code: exitCode,
+    stdout: JSON.stringify({ code }),
+    stderr: "controlled CLI diagnostic",
+  });
+
+it.each([
+  {
+    name: "mismatched target identity",
+    bytes: Buffer.from(JSON.stringify({ target_sha256: "0".repeat(64) })),
+  },
+  { name: "malformed manifest", bytes: Buffer.from("{") },
+])("checks refusal-time manifest bytes for $name", async ({ bytes }) => {
+  const path = await checkpointFile(bytes);
+  await expect(
+    assertCheckpointRefusalPreservesManifest(
+      async () => {
+        throw refusal();
+      },
+      path,
+      bytes,
+    ),
+  ).resolves.toEqual({ code: "configuration_invalid" });
+  expect((await readFile(path)).equals(bytes)).toBe(true);
+
+  await expect(
+    assertCheckpointRefusalPreservesManifest(
+      async () => {
+        // The same expected refusal must not hide replacement of the owned state.
+        await writeFile(path, JSON.stringify({ replaced: true }));
+        throw refusal();
+      },
+      path,
+      bytes,
+    ),
+  ).rejects.toThrow(/changed the checkpoint manifest/u);
+});
+
+it.each([
+  { name: "unexpected success", operation: async () => undefined },
+  {
+    name: "unrelated exit",
+    operation: async () => {
+      throw refusal("configuration_invalid", 2);
+    },
+  },
+  {
+    name: "different refusal",
+    operation: async () => {
+      throw refusal("capability_unavailable");
+    },
+  },
+])(
+  "rejects $name while checking manifest preservation",
+  async ({ operation }) => {
+    const bytes = Buffer.from("{");
+    const path = await checkpointFile(bytes);
+    await expect(
+      assertCheckpointRefusalPreservesManifest(operation, path, bytes),
+    ).rejects.toThrow();
+    expect((await readFile(path)).equals(bytes)).toBe(true);
+  },
+);
diff --git a/tests/conformance/providers/ghidra/instructionFlowVerifier.test.ts b/tests/conformance/providers/ghidra/instructionFlowVerifier.test.ts
new file mode 100644
index 0000000000..44714ed007
--- /dev/null
+++ b/tests/conformance/providers/ghidra/instructionFlowVerifier.test.ts
@@ -0,0 +1,118 @@
+import { expect, it } from "vitest";
+import { verifyGhidraInstructionFlow } from "../../../../scripts/lib/real-ghidra-instruction-flow.mjs";
+
+const leaf = { address: "0x100", value: "rea_ghidra_inventory_leaf" };
+// Static decoder controls from inventory.c; no fixture bytes are executed.
+const controls = [
+  ["0x200", "rea_ghidra_flow_return", "RET", "c3"],
+  ["0x210", "rea_ghidra_flow_cleanup_return", "RET", "c21000"],
+  ["0x220", "rea_ghidra_flow_shared_tail", "JMP", "ebfe"],
+  ["0x230", "rea_ghidra_flow_trap", "UD2", "0f0b"],
+] as const;
+
+const observedInstruction = (
+  address: string,
+  mnemonic = "RET",
+  bytes = "c3",
+) => ({
+  address,
+  status: "decoded",
+  mnemonic,
+  bytes,
+  operands: [{ raw: "0x10" }],
+  flow: {
+    kind: mnemonic === "RET" ? "return" : "branch",
+    classification_evidence: [
+      { source: "ghidra-listing-flow-type" },
+      ...(mnemonic === "RET"
+        ? [{ source: "ghidra-instruction-pcode", value: "RETURN" }]
+        : []),
+    ],
+  },
+  limitations: [],
+});
+const instructions = new Map([
+  [leaf.address, observedInstruction(leaf.address)],
+  ...controls.map(
+    ([address, , mnemonic, bytes]) =>
+      [address, observedInstruction(address, mnemonic, bytes)] as const,
+  ),
+]);
+const call = async (
+  operation: string,
+  input: Readonly<Record<string, string>>,
+) => {
+  if (operation === "read_function_instructions")
+    return { instructions: [`${input.procedure}: fixture`] };
+  if (operation === "inspect_native_instruction")
+    return input.address === "0x0"
+      ? {
+          status: "outside-memory",
+          flow: { kind: "unavailable", classification_evidence: [] },
+        }
+      : instructions.get(input.address!);
+  if (operation === "resolve_native_call_targets")
+    return { status: "not-call" };
+  if (operation === "resolve_containing_procedure")
+    return { address: input.address };
+  throw new Error(`Unexpected fixture operation ${operation}`);
+};
+const cli = async (_command: string, address: string) =>
+  instructions.get(address);
+const names = controls.map(([address, value]) => ({ address, value }));
+
+it("checks every retained inventory control for an independently parsed x86-64 ELF", async () => {
+  const result = await verifyGhidraInstructionFlow(
+    call,
+    [leaf, ...names],
+    cli,
+    {
+      format: "elf",
+      architecture: "x86_64",
+    },
+  );
+  expect(result.explicit_x86_elf_controls).toBe(4);
+  expect(result.decoded_pcode_return).toBe(true);
+});
+
+it.each(["all", "one"])(
+  "refuses %s omitted source controls on x86-64 ELF",
+  async (omission) => {
+    await expect(
+      verifyGhidraInstructionFlow(
+        call,
+        [leaf, ...(omission === "all" ? [] : names.slice(0, -1))],
+        cli,
+        { format: "elf", architecture: "x86_64" },
+      ),
+    ).rejects.toThrow(/Source fixture lacks expected decoder control/u);
+  },
+);
+
+it.each([
+  { format: "mach-o", architecture: "x86_64" },
+  { format: "elf", architecture: "arm64" },
+  { format: "pe", architecture: "x86_64" },
+] as const)(
+  "keeps controls non-applicable for $format/$architecture",
+  async (target) => {
+    const result = await verifyGhidraInstructionFlow(call, [leaf], cli, target);
+    expect(result.explicit_x86_elf_controls).toBe(0);
+    expect(result.generic_unknown_preserved).toBe(true);
+    expect(result.explicit_control_scope).toContain("Not compiled");
+  },
+);
+
+it.each([0, 1, 4])(
+  "keeps explicit unknown applicability with %i observed controls",
+  async (observed) => {
+    const result = await verifyGhidraInstructionFlow(
+      call,
+      [leaf, ...names.slice(0, observed)],
+      cli,
+      null,
+    );
+    expect(result.explicit_x86_elf_controls).toBe(observed);
+    expect(result.explicit_control_scope).toContain("Unknown");
+  },
+);