That old packaging is pretty awful anyway if you expect to access all 6 discs in arbitrary fashion.You recall correctly. However, it only has space for 6 discs (3 discs for the movies + 3 digital copy DVD-ROM discs), which still leaves one disc in the 4K set without a corresponding holder because the new edition comes with a bonus disc, in addition to the 4Ks and new BDs.
I thought about that, but I wanted to gift the old set to a friend of mine when I got the new one. It didn't feel appropriate to give her the old discs in the new packaging. If I was keeping both sets, I would probably switch them as you suggest. Since I'm not, it felt to me like the old discs really ought to go to my friend with their original packaging.