Changing the values used in the value list does not change the values stored in fields in your records. If your fields are formatted with check boxes or radio buttons, the change in the value list will hide the older values no longer in the list, but they are still present in the field.
You may need to use something such as Replace Field Contents to update the data in the field for all your records to match the new values in the value list.
That makes sence. I will create a clone of an old version of the file and inport the data into the old layout and this should solve the problem.