If you split your file into two files--one has all the data tables and the other has all the layouts, scripts, etc. You can deploy many updates just by delivering a new copy of the file that does not store the actual data tables. This is called the data separation model.
In cases where you do not use the data separation model or when you need to make changes to the data file of a split file system, you can write a script that imports all data from the current file into the new file and then updates the next serial value settings on any auto-entered serial number fields. You then deliver the new file to your client and instruct them to run this script to import the data into the new copy.
Note: to get all records imported with this script, it helps to have a script in place in the original copy that does a show all records for each table in the file. Your import script can perform this script in the original file and then it can import the data.