There are two methods that can make this workable and you will need both.
One is to create a script that imports all records from all tables of the old file into corresponding tables of the new file. Any auto-entere serial number fields would also have their "next value" settings updated in the same script so that a new record in the new copy of the file does not create a record with a serial number that matches a value in an imported record.
Optional: (But can save you a lot of time and effort deploying new updates)
The second method is to split your file into two parts on part is an interface file with all your layouts, scripts, value lists, etc. The other, the data file, has all your database tables. This is called the data separation model and when you split your file like this, you can deploy new copies of the interface file and not need to import any data, you just replace the old copy of the file with the new. This reduces the first method to being used only when changes have been made to the data file.
See this thread for more details: Convert to Seperation Model