diff --git a/src/virtualship/cli/_fetch.py b/src/virtualship/cli/_fetch.py
index cfa52a61..4eb0d2d3 100644
--- a/src/virtualship/cli/_fetch.py
+++ b/src/virtualship/cli/_fetch.py
@@ -5,7 +5,6 @@
 from pathlib import Path
 from typing import TYPE_CHECKING
 
-import click
 from pydantic import BaseModel
 
 from virtualship.utils import _dump_yaml, _generic_load_yaml
@@ -89,13 +88,10 @@ def get_existing_download(
     data_folder: Path, space_time_region_hash: str
 ) -> Path | None:
     """Check if a download has already been completed. If so, return the path for existing download."""
-    for download_path in data_folder.iterdir():
+    for download_path in data_folder.rglob("*"):
         try:
             hash = filename_to_hash(download_path.name)
         except ValueError:
-            click.echo(
-                f"Skipping {download_path.name} as it is not a valid download folder name."
-            )
             continue
 
         if hash == space_time_region_hash:
diff --git a/src/virtualship/expedition/do_expedition.py b/src/virtualship/expedition/do_expedition.py
index 1846ea14..de5d8a3a 100644
--- a/src/virtualship/expedition/do_expedition.py
+++ b/src/virtualship/expedition/do_expedition.py
@@ -32,6 +32,26 @@ def do_expedition(expedition_dir: str | Path, input_data: Path | None = None) ->
     ship_config = _get_ship_config(expedition_dir)
     schedule = _get_schedule(expedition_dir)
 
+    # remove instrument configurations that are not in schedule
+    instruments_in_schedule = [
+        waypoint.instrument.name for waypoint in schedule.waypoints
+    ]
+
+    for instrument in [
+        "ARGO_FLOAT",
+        "DRIFTER",
+        "XBT",
+        "CTD",
+        "ADCP",
+        "SHIP_UNDERWATER_ST",
+    ]:  # TODO make instrument names consistent capitals or lowercase throughout codebase
+        if (
+            hasattr(ship_config, instrument.lower() + "_config")
+            and instrument not in instruments_in_schedule
+        ):
+            print(f"{instrument} configuration provided but not in schedule.")
+            setattr(ship_config, instrument.lower() + "_config", None)
+
     # load last checkpoint
     checkpoint = _load_checkpoint(expedition_dir)
     if checkpoint is None: