diff --git a/autoconf/test_mode.py b/autoconf/test_mode.py
index 22b14ba..ece7add 100644
--- a/autoconf/test_mode.py
+++ b/autoconf/test_mode.py
@@ -64,6 +64,105 @@ def skip_latents():
     return is_test_mode() or os.environ.get("PYAUTO_SKIP_LATENTS", "0") == "1"
 
 
+def latent_nan_inject_spec():
+    """
+    Return the ``PYAUTO_LATENT_NAN_INJECT`` spec string, or ``None``.
+
+    This is a **test-only** knob used by the ``*_workspace_test`` integration
+    suites to deliberately poison latent-variable values with NaNs in an
+    arbitrary per-sample pattern, reproducing the failure mode where
+    ``compute_latent_samples`` produced ``Sample`` objects with inconsistent
+    key sets (see ``autofit/non_linear/analysis/analysis.py``). It is
+    ``None`` (a no-op) in every normal/production run because the env var
+    is unset.
+
+    Supported spec, used by :func:`inject_latent_nans`:
+
+    - ``"stride:N"`` — set NaN on column 0 of every sample whose **absolute**
+      index (across the full sample list, not the per-batch index) is a
+      non-zero multiple of ``N``. Using absolute indices makes the NaN
+      pattern straddle batch boundaries, which is the exact condition
+      needed to surface per-batch (rather than global) masking bugs.
+
+      Index 0 is deliberately **never** poisoned: with the latent batch
+      size ``B`` chosen so that ``N >= B``, batch 0 (absolute indices
+      ``0 .. B-1``) is left fully finite, so it produces samples with the
+      *complete* latent key set and seeds the latent ``Samples`` model with
+      all keys. A later batch then loses column 0 (under the buggy per-batch
+      JAX column mask), giving it a *reduced* key set — the mismatch that
+      raises ``KeyError`` in ``Samples.summary()``. Were index 0 poisoned,
+      batch 0 would itself be reduced and the mismatch would not surface.
+    """
+    return os.environ.get("PYAUTO_LATENT_NAN_INJECT") or None
+
+
+def inject_latent_nans(values_2d, start_index):
+    """
+    Apply :func:`latent_nan_inject_spec` to a materialised
+    ``(n_samples, n_latents)`` latent-value array.
+
+    Parameters
+    ----------
+    values_2d
+        A NumPy or JAX array of latent values for one batch, shape
+        ``(n_samples_in_batch, n_latents)``.
+    start_index
+        The absolute index of row 0 of ``values_2d`` within the full sample
+        list (i.e. the batch offset). NaNs are placed using
+        ``start_index + local_row`` so the pattern is consistent across
+        batch boundaries.
+
+    Returns
+    -------
+    The array with NaNs injected per the active spec. When the spec is unset
+    or unrecognised the input is returned unchanged (true no-op).
+
+    Notes
+    -----
+    Handles both NumPy and JAX arrays. For JAX the functional ``.at[...].set``
+    update is used (``jax.numpy`` imported locally, matching the library's
+    convention of never importing JAX at module scope).
+    """
+    spec = latent_nan_inject_spec()
+    if not spec:
+        return values_2d
+
+    if not spec.startswith("stride:"):
+        return values_2d
+
+    try:
+        stride = int(spec.split(":", 1)[1])
+    except (ValueError, IndexError):
+        return values_2d
+    if stride <= 0:
+        return values_2d
+
+    n_rows = values_2d.shape[0]
+    nan_rows = [
+        r
+        for r in range(n_rows)
+        if (start_index + r) != 0 and (start_index + r) % stride == 0
+    ]
+    if not nan_rows:
+        return values_2d
+
+    # JAX arrays expose ``.at`` for functional updates; NumPy arrays do not.
+    if hasattr(values_2d, "at"):
+        import jax.numpy as jnp
+
+        out = values_2d
+        for r in nan_rows:
+            out = out.at[r, 0].set(jnp.nan)
+        return out
+
+    import numpy as np
+
+    out = np.array(values_2d, copy=True)
+    for r in nan_rows:
+        out[r, 0] = np.nan
+    return out
+
+
 def with_test_mode_segment(base: Path) -> Path:
     """
     Return ``base`` with a ``test_mode`` segment appended when