At this time, the sync from Golf Genius to Whoosh does not recognize a 9-hole course or “rotated” course layout. This also applies to any event that does not use your primary course(s) Golf Genius course.
To prevent an issue when syncing a 9-hole event or rotated course, set up the pairings from the primary course for 18 holes, sync the event, and then change the pairings in Golf Genius to the correct layout.