if new save the empty dictionary to reset calibration_metadata.yml

src/cal_tools/tools.py

@@ -789,6 +789,8 @@ class CalibrationMetadata(dict):
             else:
                 print(f"Warning: existing {self._yaml_fn} is malformed, "
                       "will be overwritten")
+        else:
+            self.save()
 
     def save(self):
         with self._yaml_fn.open("w") as fd: