Shut down your dedicated servers. This is something you'll be doing a lot, so pay attention! Don't shut them down by closing the window, instead, select the window and type c_shutdown() and press the enter key. This will make sure the game saves before the server closes
If you don't get this pop-up, you will need to force an update: right click on Don't Starve Together Dedicate Server > Properties > Local Files > Verify Integrity of Tool Cache. It should work for a little bit, and then be ready to go.
But you'll probably want to customize them a little so...