diff --git a/torch_sim/runners.py b/torch_sim/runners.py
index e718577ee..4f60d3cd5 100644
--- a/torch_sim/runners.py
+++ b/torch_sim/runners.py
@@ -629,6 +629,10 @@ def optimize[T: OptimState](  # noqa: C901, PLR0915
     if isinstance(initial_state, OptimState):
         state = initial_state
     else:
+        logger.info(
+            "optimize: initializing optimizer state via chunked apply "
+            "(BinningAutoBatcher); InFlightAutoBatcher will be used for optimization"
+        )
         state = _chunked_apply(
             init_fn,
             initial_state,
diff --git a/torch_sim/trajectory.py b/torch_sim/trajectory.py
index 290351496..5a73d5802 100644
--- a/torch_sim/trajectory.py
+++ b/torch_sim/trajectory.py
@@ -186,6 +186,7 @@ def reopen_trajectories(
             ValueError: If filenames are not unique
         """
         self.finish()
+        self.trajectories = []  # drop refs so HDF5 finalizes before new opens
 
         filenames = (
             [filenames] if isinstance(filenames, (str, pathlib.Path)) else list(filenames)
@@ -524,12 +525,6 @@ def __init__(
         else:
             compression = None
 
-        # TODO FIX THIS
-        if hasattr(tables, "file") and (
-            handles := tables.file._open_files.get_handlers_by_name(str(filename))
-        ):
-            list(handles)[-1].close()
-
         # create parent directory if it doesn't exist
         filename.parent.mkdir(parents=True, exist_ok=True)
         self._file = tables.open_file(str(filename), mode=mode, filters=compression)