If you move the development site to production while you had orders coming in on your live website, you'll loose all the new data between when you got the data from the production to the development website. So I don't recommend doing that.
What we do usually is that we do a copy of the current website, test the changes we want on a copy, and then do the same changes on the live website so that we don't loose any data.
And when it's a big migration, like when we migrated from our old 1.5 website to Joomla 3.x, we actually had both websites running at the same time with a migration script we custom built for our needs in order to migrate the data in a few minutes from the old to the new website, and in the mean time, we stopped the live website to avoid loosing any orders or forum message in the process.