Here are two alternative approaches. Most developers use one, the other or a mix of the two in such situations.
1) After completing all your design changes, save a clone (no records) of your file. Take the file to work and import all records from the working copy into your clone. Update any auto-entered serial number fields to the correct next values. Swap your new file for the old. You can set this up to run with a script that moves from file to file importing and which computes and set next serial values. Thus, you can set this up to run for a few hours or even all night if necessary rather than doing it all manually table by table.
2) Split your database file into two parts: a) an interface file with all scripts, layouts, and relationships between various table occurrences and b) a data file with just the data-source tables (and some times a few other relationships so auto-enter calcs, lookups and such work). SInce most upgrades require only changes to the interface file, you can often just swap out old inteface files for new whithout having to import data whenever you have a new version to install.