unison solves this issue by specifying the symlinks explicitly in the config.
in syncthing’s case it could be done that in the folder settings a new element followSymlink (singular) is introduced, which can appear several times, e.g.
<folder id="default" path="/Users/jb/Sync/" ro="false" rescanIntervalS="60" ignorePerms="false" autoNormalize="true">
<!-- ... -->
<followSymlink>foo/bar</followSymlink>
<followSymlink>foo/bit/*</followSymlink>
<!-- ... -->
</folder>
the path names given are relative to the path attribute of the folder element.
so every time a symlink is encountered during the scan, it is matched against the list of followSymlink entries (which could also include ignore pattern style globbing), and if found, the symlink is treated like it’s target (be that a symlink, file, folder or whatever).
removing a setting after a sync of the target has been performed, would replace the file/folder on a remote device with a symlink in case symlinks are supported. so files could get lost on remote devices (if they support symlinks), but never on the local device.