The new saves will get uploaded to the Steam Cloud, yes. Losing the local saves isn't very likely unless you manually delete them. They are saved in the Documents folder on Windows -- C:\Users\(YourUserNameHere)\Documents\The Witcher 3\gamesaves
EDIT: Sorry, my mind slipped. The save location for Steam should be X:\Steam\userdata\(YourSteamAccountNumberHere)
Then it's in one of the folders there but a Google search didn't find which one.
Try taking a look in your Documents folder anyway. Some people say it should be there for the Steam version too. Let me know!