Help diagnose rclone beginner mistake

While starting to learn about rclone, I made the mistake of running the following command, as a test, from my Ubuntu home directory:

sudo rclone sync /media/foo/bar .

My assumption was that a new directory called bar would appear, but I know now that rsync would instead be trying to create a copy of the *contents* of /media/foo/bar at the second directory specified (including by deleting files). While running, I was lucky to at least be concerned at the amount of warning messages (relating to links within my git working directories), and so I hit CTRL+C to stop. I came to realise that for my usage requirements, sudo is not required; and I understand that the sync option (which is the option I want) should be used with care, and that the commands second/target directory may have files/directories deleted. As for now, and after getting rclone working nicely, I realised my earlier experiment had some unwanted side-effects. I first noticed that the .git directories of all of my git repos were gone. Then, that ~/.git-credentials was gone, and that my browser settings and passwords were gone. The basic directory structure seems unchanged. As I start to recover, can anyone advise as to which files (or directories) I should expect to be missing?