diff --git a/src/agents/pi-embedded-helpers.buildbootstrapcontextfiles.e2e.test.ts b/src/agents/pi-embedded-helpers.buildbootstrapcontextfiles.e2e.test.ts
index 64203efd8fe..9cd60cb59e0 100644
--- a/src/agents/pi-embedded-helpers.buildbootstrapcontextfiles.e2e.test.ts
+++ b/src/agents/pi-embedded-helpers.buildbootstrapcontextfiles.e2e.test.ts
@@ -89,4 +89,14 @@ describe("buildBootstrapContextFiles", () => {
     });
     expect(result).toEqual([]);
   });
+
+  it("keeps missing markers under small total budgets", () => {
+    const files = [makeFile({ missing: true, content: undefined })];
+    const result = buildBootstrapContextFiles(files, {
+      totalMaxChars: 20,
+    });
+    expect(result).toHaveLength(1);
+    expect(result[0]?.content.length).toBeLessThanOrEqual(20);
+    expect(result[0]?.content.startsWith("[MISSING]")).toBe(true);
+  });
 });
diff --git a/src/agents/pi-embedded-helpers/bootstrap.ts b/src/agents/pi-embedded-helpers/bootstrap.ts
index b2abbed7b4a..677c474b53d 100644
--- a/src/agents/pi-embedded-helpers/bootstrap.ts
+++ b/src/agents/pi-embedded-helpers/bootstrap.ts
@@ -198,12 +198,6 @@ export function buildBootstrapContextFiles(
     if (remainingTotalChars <= 0) {
       break;
     }
-    if (remainingTotalChars < MIN_BOOTSTRAP_FILE_BUDGET_CHARS) {
-      opts?.warn?.(
-        `remaining bootstrap budget is ${remainingTotalChars} chars (<${MIN_BOOTSTRAP_FILE_BUDGET_CHARS}); skipping additional bootstrap files`,
-      );
-      break;
-    }
     if (file.missing) {
       const missingText = `[MISSING] Expected at: ${file.path}`;
       const cappedMissingText = clampToBudget(missingText, remainingTotalChars);
@@ -217,6 +211,12 @@ export function buildBootstrapContextFiles(
       });
       continue;
     }
+    if (remainingTotalChars < MIN_BOOTSTRAP_FILE_BUDGET_CHARS) {
+      opts?.warn?.(
+        `remaining bootstrap budget is ${remainingTotalChars} chars (<${MIN_BOOTSTRAP_FILE_BUDGET_CHARS}); skipping additional bootstrap files`,
+      );
+      break;
+    }
     const fileMaxChars = Math.max(1, Math.min(maxChars, remainingTotalChars));
     const trimmed = trimBootstrapContent(file.content ?? "", file.name, fileMaxChars);
     const contentWithinBudget = clampToBudget(trimmed.content, remainingTotalChars);