I have a game from Steam installed on my local C drive. I bought the same game from GOG and installed on an external hard drive. (because I wanted to be able to continue playing the old version).

Two questions:

Will my Game saves for the GOG (ehd) installation, overwrite the Steam Save Data?

I ask because although I see installation files on the ehd, it still seems to be drawing the the Steam files on the C drive. I installed from GoG on the ehd , but the very first time I ran the game it showed my saved games from the other installation.

Each installation seems to work . The Gog version shows the new updated version of the game, and the Steam version shows the old version...but they both show the same saved game files.

I am trying to get the GoG version to install completely separately...and not touch or connect to the Steam installation in any way.

Is this possible?

Isn't save location usually dependent on a game? I mean, if it creates saves in "My Documents" or in "AppData", it will always do that, no matter if it was bought on Steam or GOG. So if you have it installed twice on two different drives, it should still create and load saves from the same directory. Sure, some keep saves in installation directory, but it doesn't seem to be the case here.

Steam and gog saves are compatible finally confirmed.

The games likely won't affect one another. Only the save files. So if you play on one game and use a separate save file (if available) on the second you should be fine. Or you could manually back up and manage the profile (create a folder within the save folder for each and move the save files before playing the game)

No? Why would it?

Quite often games do have a separate save game location for Steam and a different one elsewhere, and sometimes they don't. Sometimes they have the same location but there's a way to change it. There's no general rule about this; it's a case-by-case thing. What specific games are you asking about?

Where are saves located?
If it's in a user specific location then it could be as easy as creating a new user account and playing one version in that.

if it's an older game and it keeps its save data under its installation directory and that's as complicated as it gets then it won't be a problem because the Steam game's saves will be under Steam's directory or one of its libraries and gog will have its own (unless you're installing your gog games to Steam's directory haha).

if it's a newer game and it uses Documents or AppData to store its stuff then it is possible for there to be conflict but you should also be able to manage those saves through the game. the only ones you might lose are autosaves if there is anything like that. it would depend on the save system written into the game.

finally, some games use the registry for some things and even if they directories didn't come into conflict, it's possible that that could.

just go pcgamingwiki, find out what's going on with the saves for this game, and back those up.