Server Help Backing Up Server - Questions on Mechanics

Thanks in advance for the help. I'd like to periodically back up my server files for DR. I don't want any of my players to lose their progress and hours of work if something happens to my server. I have a couple questions about how to do this.

First, how does the game write changes to local files? Are they updated in real-time or does that happen periodically? Do I need to issue some kind of console command to write recent changes to files? I want to make sure that the files are updated before I back them up.

Second, are all my server "world" files located in the \Storage\universe subfolder of my Starbound folder or are there other files I would need to preserve in order to restore the server "world"?

EDIT: It looks like the server must be stopped in order to back its files up. I tried a copy and noted that \storage\universe.chunks, \storage\universe.lock and \storage\starbound_server.log are all in use (unsurprisingly).