I followed this forum's suggestion to delete the steam cloud data and write protect the folder so it can't replace them to stop it from overwriting my saves with the first saves ever made. There is no option to disable this, write protecting the folder was the simplest way to stop it from doing this very unwanted action.

Since the last patch it makes me confirm four or five times that yes I want to play even though it can't sync steam cloud. Did they fix it or what changed that today it makes me confirm this five times in a row but yesterday it would just give up and run with no problems? I do not want to un-write-protect it if it is just going to "helpfully" remind me of my saves at level 1 in the tutorial constantly.

Yes, they fixed it a few days ago.