I am running a similar scenario, but I am using a Cloud Provider for my production environment, in order that I do not need to care about replication of DB, multi server instances etc. (I am Using pagodabox, but AWS would also work perfectly fine).
I would recommend you to create real migrations for Database Migrations, in order to track those via svn or something else. In that case, you can also provide information, how to roll back. I am using https://github.com/doctrine/migrations, but mainly because I use doctrine as ORM.
If you have a migration tool, you can easily add a command in your deployment script to run those migrations after deployment.
I don't think that the database synchronisation is a big issue during deployment. That might depend on the actual infrastructure youre using. The cloud providers like pagoda or aws take care of it for you.