You don't need to export, just import. You can set up a script that imports all the data from all the tables in the old copy into an empty copy of the new. You do have to take the file offline so that no changes are made while the data is being imported to make sure that all data in the new version is complete.
And it is a very good idea to take back up copies of your files and run your script, then make exhaustive tests on the result before doing it 'for real' on your client's current copy of the file.
In addition to importing data, any fields that auto-enter a serial number should also have their 'next serial value' updated in the same script.
In the future, you might split these files into interface and data files--which is called the Convert to Seperation Model, to reduce the instances where you need to import data from one file to another.