I bought my copy of SS before the Steam release but later went on to install via Steam. I sometimes accidentally click on the shortcut to the *.exe in the Windows start menu by mistake, instead of the one that says steam://rungameid/xxxxx and only realise the mistake when the saved game opens in a weird condition, like map centered on the Dawn Machine and ship can’t move.
Is the Steam thing just a shortcut that eventually points at the *.exe in the original folder, or is it actually a whole separate installation? If I uninstall Sunless Sea in Windows > Control Panel > Programs what happens?