Instant Scenery only places library objects into a scene, so the resulting BGL files should not affect anything important.
That said, you should NEVER have run Instant Scenery in this FS session when testing anything. Always restart FS and get a fresh FS program - IS changes many things in the FS visual world. For example, shadows may disappear for any objects being displayed by IS, often autogen buildings that have been excluded may reappear, and animated objects may be oddly "exploded". Always restart and be safe.