Well, then they have to be replaced. The Xilinx parts are one time programable the Atmel parts are Flash based and are reprogramable.
All the cards delivered by VT had two chips on them at this location because of the price.
These chips are simply chained and can be replaced by one larger(content) chip. So you can use a single xc17256 or an atmel counterpart instead of the two smaller ones.
You could also use two xc17128's.
As long as they provide enough memory you could use any combination as long as the first chip is completly programmed and the last one holds the rest that didn't fit in the first one.