diff --git a/giant/data/dataset.py b/giant/data/dataset.py
index ce05905..afdb051 100644
--- a/giant/data/dataset.py
+++ b/giant/data/dataset.py
@@ -109,6 +109,7 @@ class StreamingStepsDataset(IterableDataset):
                     cond_normalizer=self.cond_normalizer,
                     target_normalizer=self.target_normalizer,
                     proc_map=self.proc_map,
+                    require_secondaries=True,
                 )
                 buf_cont.append(cond_cont)
                 buf_cat.append(cond_cat)
diff --git a/giant/data/transforms.py b/giant/data/transforms.py
index e8df166..4567fff 100644
--- a/giant/data/transforms.py
+++ b/giant/data/transforms.py
@@ -434,6 +434,7 @@ def build_features(
     target_normalizer: Normalizer | None = None,
     fit: bool = False,
     proc_map: dict[str, int] | None = None,
+    require_secondaries: bool = False,
 ) -> tuple[
     np.ndarray,
     np.ndarray,
@@ -455,6 +456,11 @@ def build_features(
     proc_idx: (N,) integer process-class label (ProcessRouter supervision only —
               never conditioning). Zeros when `proc_map` is None or the loaded
               data has no "process" column (e.g. pre-conversion parquet files).
+
+    require_secondaries: when True, raise if any step has n_sec > 0 but the
+        per-secondary list columns are absent (a mis-converted file that would
+        otherwise silently zero all Stage-2 targets). Training paths set this;
+        Stage-1-only callers (e.g. `giant predict`) leave it False.
     """
     from giant.constants import K_MAX
 
@@ -515,6 +521,25 @@ def build_features(
             sec_pdg_list
         ).astype(np.int64)
     else:
+        # Guard against silently training Stage 2 on zeroed targets: if any step
+        # actually spawned secondaries (n_sec > 0, from child_track_ids) but the
+        # per-secondary columns are absent, the file was never run through the
+        # parent->child join (steps_to_parquet._add_secondary_attributes /
+        # `dwarf convert`). Zero-filling here would collapse every secondary to
+        # PDG index 0 and a constant energy fraction — a broken Stage 2 with no
+        # error. Callers that only need Stage-1 (e.g. `giant predict`) keep the
+        # default require_secondaries=False.
+        if require_secondaries and n_sec_raw.max(initial=0) > 0:
+            n_with_sec = int((n_sec_raw > 0).sum())
+            raise ValueError(
+                f"{n_with_sec} step(s) have secondaries (n_sec > 0) but the "
+                "per-secondary columns (sec_E_list / sec_pdg_list / sec_dx_list "
+                "…) are missing. This parquet was not run through the "
+                "parent->child join (steps_to_parquet._add_secondary_attributes "
+                "/ `dwarf convert`); training on it would silently zero all "
+                "Stage-2 targets. Re-convert the file, or pass "
+                "require_secondaries=False for Stage-1-only use."
+            )
         N = len(n_sec)
         sec_cont = np.zeros((N, K_MAX, 4), dtype=np.float32)
         sec_pdg_idx = np.zeros((N, K_MAX), dtype=np.int64)
diff --git a/giant/pipeline.py b/giant/pipeline.py
index 931c5fd..c06d49f 100644
--- a/giant/pipeline.py
+++ b/giant/pipeline.py
@@ -72,7 +72,10 @@ def run_train_job(
                 continue
             chunk_tr = {k: v[mask] for k, v in chunk.items()}
             cond_cont, _, target_s1, _n_sec, _sec_cont, _sec_pdg, _proc, _, _ = (
-                build_features(chunk_tr, pdg_map, mat_map, proc_map=proc_map)
+                build_features(
+                    chunk_tr, pdg_map, mat_map, proc_map=proc_map,
+                    require_secondaries=True,
+                )
             )
             cond_acc.update(cond_cont)
             tgt_acc.update(target_s1)
diff --git a/tests/test_transforms.py b/tests/test_transforms.py
index ad8ddfb..7c5eed8 100644
--- a/tests/test_transforms.py
+++ b/tests/test_transforms.py
@@ -280,3 +280,30 @@ def test_build_features_proc_idx_looks_up_proc_map():
     *_, proc_idx, _, _ = build_features(data, pdg_map, mat_map, proc_map=proc_map)
 
     np.testing.assert_array_equal(proc_idx, [0, 1, 2])
+
+
+def test_build_features_require_secondaries_raises_when_lists_missing():
+    """A parquet with n_sec > 0 but no per-secondary list columns was never run
+    through the parent->child join; require_secondaries must catch it instead of
+    silently zeroing every Stage-2 target (regression: this collapsed the
+    secondary species to a single PDG index during training)."""
+    data = _minimal_step_data(3)
+    data["n_sec"] = np.array([0, 2, 1], dtype=np.int32)  # secondaries, but no lists
+    pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
+
+    with pytest.raises(ValueError, match="per-secondary columns"):
+        build_features(data, pdg_map, mat_map, require_secondaries=True)
+
+
+def test_build_features_require_secondaries_ok_when_no_secondaries():
+    """require_secondaries only fires when secondaries actually exist; a file
+    with n_sec == 0 everywhere (e.g. Stage-1-only) must still load."""
+    data = _minimal_step_data(3)  # n_sec all zero
+    pdg_map, mat_map = {11: 0}, {"PbWO4": 0}
+
+    _, _, _, _, sec_cont, sec_pdg_idx, *_ = build_features(
+        data, pdg_map, mat_map, require_secondaries=True
+    )
+
+    assert not sec_cont.any()
+    assert not sec_pdg_idx.any()