One theory would be that somehow it decided that the Mac was the more up to date copy. Since there were no files, it concluded they must have been deleted, and so does the same on the cloud copy. I don't know why it would decide the Mac was more up to date though.
Earlier sync tools like rsync can do the same, but only if you pass an option telling it you really want to delete files
AFAIK rsync has always been uni-directional, so I don't think there can be an equivalent. If you run `rsync -av --delete local://foo cloud://foo`, you are very explicit that you want files on the the cloud to be gone if they don't exist locally.
Earlier sync tools like rsync can do the same, but only if you pass an option telling it you really want to delete files