Baronlando said:

Lucas isn't always clear when he talks, he may have meant some kind of intermediate IN or IP that yielded foreign subtitled prints in that part of the world, not that actual theater prints were used in 1997. I don't think they would have been able to integrate that back then.

Yeah, its impossible to say what he is really talking about there but IP's or IN's in European countries sounds like an likely scenario where they had no other options, no way they ended up using release prints.

EDIT: He doesn't even say that he went there to retrieve prints, his words was "I had to go to Poland and Czechoslovakia. Putting things together."

And despite him saying that the separations was worthless, other reports states they did actually use them to restore various sections of the film. And while color registration issues may have been a huge obstacle back in the early nineties, digital tools have made it possible to overcome potential color misalignment issues.