You either a] develop on the soltuion live 2] use the separation model 3] import all their data into your latest copy. There is no such thing as merging two filemaker files.
I clone the product database, made all change.
After some times, I copy the product database for test, and finally, I close for a while the access to the product base.
I empty the dev database and inport inside all datas of the product's one.
Sometines must use some scripts to agreate or made calculation on new datas. When all is done, I gain access to the product database.
You can do this two times to check the new solution with recent datas and when you are convinced that all is ok, you backup the product database and made what was describe above.
We've written a product to do exactly this. It's designed to build you an importer that you can then control and monitor the whole process with : www.goya.com.au/refreshfm
We had the same issue with managing solutions for many clients, and wanting to do updates in the shortest amount of time with the least room for issues.