diff --git a/bqskit/passes/io/checkpoint.py b/bqskit/passes/io/checkpoint.py
index 7a7dbd776..a374cbb85 100644
--- a/bqskit/passes/io/checkpoint.py
+++ b/bqskit/passes/io/checkpoint.py
@@ -54,5 +54,6 @@ async def run(self, circuit: Circuit, data: PassData) -> None:
         with open(self.checkpoint_filename, 'rb') as f:
             checkpoint = pickle.load(f)
             circuit.become(checkpoint[0])
-            data.clear()
-            data.update(checkpoint[1])
+            new_data = PassData(circuit)
+            new_data.update(checkpoint[1])
+            data.become(new_data)