This info is for PC Users.
Steam Cloud Saves
Be aware that Steam Cloud may corrupt or not save your game file in rare situations. This has happened to me, and I lost 8 hours worth of gameplay. Could not find the files on my PC nor could I find them in my Steam Account, even checking my remote Steam storage.
You do have the option to switch off cloud saves and save the game files directly on to your computer via teh games properties in your steam account.
Icarus Missions
If you DO NOT have the Mission Structure Cleanup enabled under the World Map Settings, failing a mission and restarting the same missions will apply a new set of structures spawned above the old structures.
Why Does this matter?
Example: On the Promethus Map when you activate the Mission Dispatch on Hard Mode you need to power up the power plant. If you fail this mission or cancel and reactivate it then you are going to have a new set of structures spawning above the current ones.
In this case 2 power plants and when you attempt to wire these up there will be a conflict between both power plants. The one you see and the one that was from the previous failed mission. This in effect, lost me 4 plus hours of game time, and I was experienced enough to know how to reset my game to a previous save.
Copy Pasting Prospect Files
Do these at your own peril for whatever reason that may be.
I only do this if I am starting a new playthrough and need some game oriented stuff set to zero.
But be warned do not keep the copied files in the same prospect directory otherwise when you are in the World Load Up screen you will see multiple map instances.