I know right now rclone sync will not current remove a target folder if it is to be replaced by a source link (even with --links option). Post here and my own experience.
However, --delete-before does work around this. The target folder is removed first and then later in the sync process the link gets put into the target.
It would be great if there was a way to force --delete-during (default) to also remove the target folder and replace with link. Even better if the target folder was removed in the background ... something like "mv target/folder target/folder.deleteme; ln -s <source_link_target> target/folder; rm -rf target/folder.deleteme &". This would minimize the target folder "missing" to a very brief window which is ideal for more "live" updates of a target.