As long as you update it to the correct install location there shouldn't be any conflict.
That didn't matter. The path was correct on both apps, but Steam corrupted the ED application when it attempted to update over the Launcher's update.
It has something to do with file sync or something like that according to FDEV support. My ED app got corrupted when Steam tried to update itself after the update that was downloaded by the Launcher. FEDV advised to never use the Launcher and always use Steam.
I took their advice, since I had to reinstall the entire game to fix that problem. (This was at the 2.4 update)
or... You could roll the dice and hope that the same issue never happens to your installation of the game.
