Man I get paranoid about synchronization programs for this very reason. There's usually some turnkey easy-mode enabled as soon as you first launch that's like:
"Hey you wanna back up your entire NAS to your phone?! That'll be fun, right?!"
And you're like "...No."
And then it wants to obliterate everything so it's all "synchronized", often it's not easy to find a "No, stop, don't do anything at all until I configure this." Option.
iTunes was SO BAD about this.
Syncthing is the least-bad sync software I've ever run. It's got some footguns but it's still brilliant.
I would imagine there's still ways to back up version controlled software right?
iTunes would stomp all over your hard drive, fucking up every MP3 file it could find, and then refuse to believe you could have one copy of a file. Either it's on your iPod and your computer, or it's getting dragged behind the woodshed.
Give me sync software that only ever increases redundancy.