You have have both. The selection is on the start menu when you start a new game.

You can play both. The version is baked into your save game.

It is recommended to completely close the game if you are switching from one to the other.

Originally posted by Loyd:

It is recommended to completely close the game if you are switching from one to the other.

I would say it's more than recommended, it's a must situation. Make sure you completely close the game and restart whenever switching Scenarios.

I think you are all missing his point - or I am now... :
You cannot play your savegames from vanilla Empyrion (which means: without Reforged Eden). You have to install the Scenarion and then start a new Game via "new Scenario" .
Your save games are not exchangeable between the original game and Reforged Eden.

edit: Ah, OK: after reading the question for the fourth time I just realized: Yes, I was missing his Point here...
So: Yes, you can still play your old save games with your friends after downloading Reforged Eden. Your old saves are loaded as a normal game, the new ones are loaded as a scenario. Sorry for the hickup :)

Even says it in the top of the description:

Getting started:
To start playing Reforged Eden, subscribe to the scenario and then go to new game > scenarios > select Reforged Eden. You can start the scenario in creative by clicking on "game mode". Reforged Eden will only apply to save games started using the scenario and will not affect your other saves.