This is exactly why syncthing is problematic as a backup solution.
If I delete a file on one host and syncthing is doing the default two way sync, the deletion is also replicated to the other machine.
They acknowledge this in their faq: https://docs.syncthing.net/users/faq.html#is-syncthing-my-ideal-backup-application
You can mitigate some of these issues with file versioning, or one way syncs, but ultimately it's just not really the tool for the job.