I would recommend having only one version. At the moment, if you have both versions, the Steam saved data has priority. This means that everytime you launch the game on Steam, the DRM-Free version saved data will be replaced by the Steam saved data. It works that way because a DRM-Free version wasn't planned to begin with, so the saved file is the same for both versions. And, for now, I don't have time to rework the save system, sorry.
No worries, it's just good to have this information at all.
Not many devs actually tell it and we have to find it out for ourselves.
Though there is advantages to having a copy on both platforms as installing on multiple machines can be more a hassle with Steam than just being able to use a DRM version instead as an option.
Installing both versions at once isn't too common but knowing how the save files work it can be worked around since we now know when best to back it up.
Really wish save file information had a section in game descriptions or something always have to dig those things up or guess as every game does something different.
Again thanks for being open and honest about it, most appreciated.