Since it seems impossible to simply copy a script, a table, etc. and have him replace it on his, this has been at time frustrating and error prone.
With FileMaker Advanced, these are not impossible things to do in FileMaker. You can copy and paste script steps and field definitions from one file to another using FileMaker Advanced.
But I think that converting your solution to fit the Convert to Seperation Model will help with the maintenance issues. This sets up a solution of two files, one with all the scripts, layouts, value lists, etc and one with the all the data tables and data level relationships. Any time that you modify the interface file, your client can simply swap out the old copy for the new.
But for the less frequently needed updates of data tables and data level relationship changes, you can send the client a clone copy (no records in the file) with a script that uses Import Records and Set Next Serial value to copy over all records from all tables and to update the serial number settings on any auto-entered serial numbers.