It's not that the flatbeds have been removed, it is simply that the aircraft have been grounded and smaller aircraft have been subbed in. The -800 doesn't have flatbeds but has the reduced capacity to support the route.
Based on the investor advice given by all three legacy carriers yesterday about a "tough fall," it would not surprise me to see the smaller aircraft stay in place. It's unfortunate, but many are predicting 18-24 months before consumer demand returns.