New installs shouldn't come with saves, so I am not sure what happened. Sometimes, there are issues with files being set to "read-only", and that can delete files when you try to save over an old file. A similar thing can happen if the game is installed in a folder which doesn't give you full access.
Other than trying to recover the lost files with a program like recuva, and maybe move the game to a different folder (like, something inside documents) to test if it happens again, I don't know what you could do.