diff --git a/python/lean_pool/indexes.py b/python/lean_pool/indexes.py
index 6b5c9dfb14..66c7459182 100644
--- a/python/lean_pool/indexes.py
+++ b/python/lean_pool/indexes.py
@@ -18,8 +18,8 @@
     "Released under Apache 2.0 license as described in the file LICENSE.\n"
     "Authors: Lean Pool contributors\n-/\n" + MODULE_HEADER + GENERATED_MARKER
 )
-# Removed after the separate content migration has landed.
-REQUIRE_PROJECT_ROOTS = False
+# Production module-system packages must never revert to a flat index.
+REQUIRE_PROJECT_ROOTS = True
 
 
 def project_modules(root: Path) -> dict[str, list[str]]:
diff --git a/python/tests/test_rebase_fastpath.py b/python/tests/test_rebase_fastpath.py
index b3a87cd3db..2aa9cfb04f 100644
--- a/python/tests/test_rebase_fastpath.py
+++ b/python/tests/test_rebase_fastpath.py
@@ -48,7 +48,7 @@ def rebased(tmp_path: Path) -> tuple[Path, str, str, str, str]:
     (root / "LeanPool/A.lean").write_text("module\n")
     (root / "LeanPool/projects.yml").write_text("projects:\n  - slug: a\n")
     for name in rebase_fastpath.PINNED_INPUTS:
-        (root / name).write_text(name)
+        (root / name).write_text('name = "test"\n' if name == "lakefile.toml" else name)
     _index(root)
     old_base = _commit(root, "base")