Issues with syncing

One way to do this is by ignoring some Obsidian files, like already suggested by @gadget .

Another way it to use the Syncthing API to revert local changes programmatically. Read more here: Revert Local Changes from command line?

Either way you have some work to do, because the use case you seem to be after (synchronized copy which shall revert local changes) is something which Syncthing cannot do out of the box. This is a conscious design decision. Your use case is natively supported by e.g. rsync.