diff --git a/src/domain/process/processCapture.validation.test.ts b/src/domain/process/processCapture.validation.test.ts
index a24b983807..9a99f257d2 100644
--- a/src/domain/process/processCapture.validation.test.ts
+++ b/src/domain/process/processCapture.validation.test.ts
@@ -288,6 +288,75 @@ it("binds unfollowed coverage to observed symlink metadata without inventing an
   ).toThrow("enumeration_omissions");
 });
 
+it("requires top-level filesystem facts to match their checkpoints", () => {
+  const baseline = emptyCapture();
+  const file = {
+    path: "root_0:created.txt",
+    type: "file" as const,
+    mode: 0o100644,
+    size: 4,
+    sha256: "b".repeat(64),
+    symlink_target: null,
+  };
+  const effect = {
+    path: file.path,
+    status: "created" as const,
+    before: null,
+    after: file,
+  };
+  const topLevelOnly = {
+    ...baseline,
+    files_after: [file],
+    filesystem_effects: [effect],
+    truncation_details: {
+      ...baseline.truncation_details,
+      filesystem_after: {
+        ...baseline.truncation_details.filesystem_after,
+        hashed_bytes: 4,
+      },
+    },
+  };
+  const consistent = {
+    ...topLevelOnly,
+    filesystem_checkpoints: baseline.filesystem_checkpoints.map((checkpoint) =>
+      checkpoint.name === "after_settlement"
+        ? { ...checkpoint, files: [file], effects: [effect] }
+        : checkpoint,
+    ),
+  };
+  expect(parseProcessCapture(consistent)).toEqual(consistent);
+  const withCheckpointFiles = (
+    name: string,
+    files: (typeof baseline.files_before)[number][],
+  ) =>
+    consistent.filesystem_checkpoints.map((checkpoint) =>
+      checkpoint.name === name ? { ...checkpoint, files } : checkpoint,
+    );
+  for (const contradictory of [
+    topLevelOnly,
+    { ...consistent, filesystem_effects: [] },
+    // File lists alone disagree; effects still match.
+    {
+      ...consistent,
+      filesystem_checkpoints: withCheckpointFiles("after_settlement", []),
+    },
+    {
+      ...consistent,
+      filesystem_checkpoints: withCheckpointFiles("before", [file]),
+    },
+    {
+      ...baseline,
+      filesystem_checkpoints: baseline.filesystem_checkpoints.map(
+        (checkpoint) =>
+          checkpoint.name === "before"
+            ? { ...checkpoint, effects: [effect] }
+            : checkpoint,
+      ),
+    },
+  ])
+    expect(rejectedPaths(contradictory)).toEqual(["filesystem_checkpoints"]);
+});
+
 it("never considers truncated captures equivalent", () => {
   const complete = emptyCapture();
   const capture = {
diff --git a/src/domain/process/processCaptureValidation.ts b/src/domain/process/processCaptureValidation.ts
index b64ed1083e..fe6d08f3bd 100644
--- a/src/domain/process/processCaptureValidation.ts
+++ b/src/domain/process/processCaptureValidation.ts
@@ -1,3 +1,5 @@
+import canonicalize from "canonicalize";
+
 import {
   digestProcessCommitment,
   processScenarioOutputBudgetProjectionSchema,
@@ -20,6 +22,11 @@ type RequireInvariant = (
   message: string,
 ) => void;
 
+const sameJsonValue = (left: unknown, right: unknown): boolean => {
+  const encoded = canonicalize(left);
+  return encoded !== undefined && encoded === canonicalize(right);
+};
+
 const orderedTimestamps = (values: readonly number[]): boolean =>
   values.every((value, index) => {
     const previous = values[index - 1];
@@ -254,6 +261,15 @@ const validateLifecycle = (
   ), "filesystem_checkpoints", "filesystem snapshot times must be ordered");
   require(!capture.filesystem_checkpoints.some(({ truncated }) => truncated) ||
     capture.truncated, "truncated", "filesystem snapshot truncation must propagate to the capture");
+  // Comparison reads only the checkpoints, so the top-level copies must not disagree.
+  const [initial, final] = capture.filesystem_checkpoints;
+  require(sameJsonValue(initial?.files, capture.files_before) &&
+    initial?.effects.length === 0 &&
+    sameJsonValue(final?.files, capture.files_after) &&
+    sameJsonValue(
+      final?.effects,
+      capture.filesystem_effects,
+    ), "filesystem_checkpoints", "top-level filesystem snapshots and effects must match the initial and final checkpoints");
   require(capture.exit.reason === "exited" ||
     capture.exit.code ===
       null, "exit", "deadline termination cannot declare a normal exit code");