Unfortunately there is currently an issue with the way that Factorio saves for multiplayer servers. It works by saving the loaded world to three autosave files (_autosave1,_autosave2,_autosave3) Instead of to it's loaded world (DefaultWorld by default).
Should yours go offline for any reason, when it loads it will load the DefaultWorld fresh again.
The best way to combat this is to do one of the following:
1. Save your game manually using the ingame console and running this command - /c game.server_save() when you have finished playing or plan on turning the server offline.
2. Change your loaded world to "_autosave1" and the save interval to 1 (minute) This will mean that your server will load the created autosave and increase the rate at which it autosaves. Your server will then autosave every 3 minutes. You can do this by going to "Edit profile" in your clanforge control panel. Scroll to the bottom of the base and you will see the option to change the world name and save interval.