It really could be anything. It could be something simple, like a change in format; or it could be something huge, like a change in how objects are represented. This comment in FRED could be a clue:
* 25 3/04/97 6:27p Hoffoss
* Changes to Fred to handle new wing structure.
That would be a reorganization, but it would be on the simpler side. Hypothetically, I could picture a situation where wings and the ships they contain would get all tangled up. They could be untangled with a little bit of effort, but it's certainly possible that the mission designers wouldn't know how to do that and the programmers would have more pressing priorities. As a result the old missions would never have been ported over.
I have a hunch that "La Ruota della Fortuna", which happened to be authored by Duncan McPherson, is the rebuilt version of the original mission. Just as described in the blog, the player expects one thing but arrives to find something completely different, and the mission quickly turns into a big furball.