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Look into the Seperation Model. I usually have at a minimum, Data, User Interface, and Reports.
Most of the changes tend to be in a User Interface or Reports.
If you do have to update the data portion of your system, you can create a script that performs imports on each table in turn and then updates the serial number settings on any serial number fields. Work for you to set up, but not difficult for your clients to use to update their files.
Thanks for the tips.