Upload a save: from the Server Manager in-game, use Manage Saves → Upload and pick a save from your PC. Or stop the server and upload the .sav file to .config/Epic/FactoryGame/Saved/SaveGames/server/ in Files, then load it from the Server Manager.
Autosaves: the server autosaves every 5 minutes and keeps 3 autosaves by default (Startup page: Autosave Interval, Num Autosaves). Download a save from the Server Manager any time to keep a copy.
