diff --git a/src/glide/cli.py b/src/glide/cli.py
index f05baf9..c044cce 100644
--- a/src/glide/cli.py
+++ b/src/glide/cli.py
@@ -266,9 +266,11 @@ def merge(
     dataset_dims = set(ds.dimensions)
     ds.close()
 
-    if dataset_dims == {"time"}:
+    if (dataset_dims == {"time"}) | (dataset_dims == {"time", "time_uv"}):
         input_file_level = 2
-    elif dataset_dims == {"profile_id", "z"}:
+    elif (dataset_dims == {"profile_id", "z"}) | (
+        dataset_dims == {"profile_id", "z", "time_uv"}
+    ):
         input_file_level = 3
     else:
         raise ValueError(
diff --git a/src/glide/process_l3.py b/src/glide/process_l3.py
index b138344..699e28f 100644
--- a/src/glide/process_l3.py
+++ b/src/glide/process_l3.py
@@ -42,7 +42,7 @@ def bin_q(
         ds[v] = (
             dims,
             np.full_like(ds.conductivity.values, np.nan),
-            config["variables"][v]["CF"],
+            config["merged_variables"][v]["CF"],
         )
         # Dissipation rate is stored in the q file as the log10 of the value.
         # Convert it to the actual value.
@@ -61,7 +61,10 @@ def bin_q(
                 ds_.profile_time_end.astype("M8[s]"),
             )
         )
-        if eds_.e_1.size < 1:
+        # Filter to valid depths within the bin range (also drops NaN).
+        in_range = (eds_.depth >= depth_bins[0]) & (eds_.depth <= depth_bins[-1])
+        eds_ = eds_.sel(time=in_range)
+        if eds_.time.size < 1:
             _log.debug("No epsilon data")
             continue
         binned = eds_.groupby_bins("depth", depth_bins).mean()