I started playing when 0.5 was out and when I downloaded 0.6 it just kept my saves. Even after I deleted 0.5 my saves were still on 0.6 so I'd assume you wont have to do anything at all.
If you go into the Eternum folder and open the game folder, you'll see another folder named "saves". You can copy paste save files in that folder from prior versions to your newly updated version.
