I watched the special feature talking about production of the miniseries and they seemed to hint at that Pilot's set wasn't destroyed, that they loved him after all these years and he's still great. Maybe they stuck it together wrong. I didn't notice any big chances, maybe they needed to make it smaller?
There's one shot in particular in the movie where the Eidolon is being introduced to Pilot and it's noticeable that the set isn't the same. I'd copy/paste it but that's a lot of work.