Using Heidi in migrating between servers

I would like to use Heidi to migrate between servers. So an initial export from the live server. Then setting up the new server. This is all clear.

And when all is done I would like to export the DB again and update the small changes (new registrations ect). Can this be done and how, or what should I search for?

DB is 1,8 gb. Just updating will save me time I guess and makes the downtime minimal. Other option workaround was to remove the first database and then just replace it.