diff --git a/scripts/submit.py b/scripts/submit.py
index 5087eac..89f4faf 100644
--- a/scripts/submit.py
+++ b/scripts/submit.py
@@ -122,7 +122,7 @@ def main() -> None:
         prefetch_assets(config)
 
     # Set up the run directory (so the SLURM script can reference it).
-    run_dir = setup_run_directory(config)
+    run_dir = setup_run_directory(config, allow_override=True)
     logger.info("Run directory: %s", run_dir)
 
     if not confirmed:
diff --git a/src/post_training/utils/paths.py b/src/post_training/utils/paths.py
index a46a89d..9a0277f 100644
--- a/src/post_training/utils/paths.py
+++ b/src/post_training/utils/paths.py
@@ -33,7 +33,7 @@ def generate_run_name(config: PostTrainingConfig) -> str:
     return get_backend(config.backend).generate_run_name(config, timestamp)
 
 
-def setup_run_directory(config: PostTrainingConfig) -> Path:
+def setup_run_directory(config: PostTrainingConfig, allow_override: bool = False) -> Path:
     """Create the run output directory tree and return the run root.
 
     Directory layout::
@@ -58,8 +58,13 @@ def setup_run_directory(config: PostTrainingConfig) -> Path:
 
     run_dir = base / run_name
 
-    # Handle debug override.
-    if config.debug.enabled and config.debug.override_existing and run_dir.exists():
+    # Handle debug override — only when submit.py explicitly opts in.
+    if (
+        allow_override
+        and config.debug.enabled
+        and config.debug.override_existing
+        and run_dir.exists()
+    ):
         shutil.rmtree(run_dir)
 
     from post_training.backend import get_backend