That only happened to me once (when I was initially setting up Syncthing), but even once is too often for something like this.
The incredible part for me is that there was no clear indication in the UI that I was doing something destructive, I only realized that Syncthing was destroying my files because I was manually keeping an eye on it through my file browser. Surely deleting local files should require the user to first confirm using large warnings and red buttons?!
I sync my org files using a low-tech solution: I have a .dir-locals file that injects a post-save hook that automatically commits changes to git and pushes them to the remote. It's stupid, but it works, and I never have to think about it.
I do take regular backups to Blu Ray optical disks 'just in case' but have yet to have need of them.
The implementation of the actual sync is pretty good (I never had a problem with it).
But, the UI is not intuitive at all. Its hard to setup a new sync, and if you're not careful you can set it up in a way that deletes all your files without any warning.
Software UI is hard, that's it.
If anything, it is the UI of Synctying that allows me (sometimes) to try and protect some directories.
When the same thing happens with Dropbox, all my computers automatically lose all files because there is no way to force a one directional sync to one specific directory.
I have a git alias setup called "git autopush" that adds all, commits with a generic "[autopush]" message, and pushes to the upstream remote. I use this for my repos of "running" files like org files etc. I've modified it recently to require a config param to explicitly enable it because I'm afraid of typing it in work repos :)
Last time, I configured a Receive only folder in device Y, but forgot to mark it as "shared to device Y" in device X's settings.
Net result: directory erased in device Y.
Sure, I still had the copy in device X, but that was gigabytes that needed copying around, a couple hours of wasted time. It's just mind boggling that Syncthing would happily go around deleting thousands of files without warning specially with a minor config error .