diff --git a/janus_core/cli/phonons.py b/janus_core/cli/phonons.py
index 48c82341..fb3e200a 100644
--- a/janus_core/cli/phonons.py
+++ b/janus_core/cli/phonons.py
@@ -232,7 +232,6 @@ def phonons(
     from janus_core.cli.utils import (
         carbon_summary,
         check_config,
-        dict_tuples_to_lists,
         end_summary,
         parse_typer_dicts,
         save_struct_calc,
@@ -356,9 +355,6 @@ def phonons(
         log=log,
     )
 
-    # Convert all tuples to list in inputs nested dictionary
-    dict_tuples_to_lists(inputs)
-
     output_files = phonon.output_files
 
     # Save summary information before calculations begin
diff --git a/janus_core/cli/utils.py b/janus_core/cli/utils.py
index c30f568e..f89b7132 100644
--- a/janus_core/cli/utils.py
+++ b/janus_core/cli/utils.py
@@ -56,9 +56,11 @@ def dict_tuples_to_lists(dictionary: dict) -> None:
     """
     for key, value in dictionary.items():
         if isinstance(value, dict):
-            dict_paths_to_strs(value)
+            dict_tuples_to_lists(value)
         elif isinstance(value, tuple):
             dictionary[key] = list(value)
+        elif isinstance(value, list):
+            dictionary[key] = [list(x) if isinstance(x, tuple) else x for x in value]
 
 
 def dict_remove_hyphens(dictionary: dict) -> dict:
@@ -172,13 +174,19 @@ def start_summary(
     output_files
         Output files with labels to be generated by CLI command.
     """
+    # Prevent modification of calculation inputs
+    inputs_copy = inputs.copy()
+
     output_files["summary"] = summary.absolute()
     dict_paths_to_strs(output_files)
 
+    # Convert all tuples to list in inputs nested dictionary
+    dict_tuples_to_lists(inputs_copy)
+
     save_info = {
         "command": f"janus {command}",
         "start_time": datetime.datetime.now().strftime("%d/%m/%Y, %H:%M:%S"),
-        "inputs": inputs,
+        "inputs": inputs_copy,
         "output_files": output_files,
     }