You're instinctively assuming several things that shouldn't be assumed. Even more amusing, a lot of the problems will come from programmers assuming things that were perfectly fine to assume as long as they decided no different versions would play together, and that's the most common way to do things in videogames because it works.
First, that just taking away that chunk has no repercussions for other bits. That entirely depends on their scripting and how their data is organized. To take an extreme example, each object could be referred in-game by an ID based on their position in a table of contents. Remove one chapter of the table, and all the objects after that have new IDs and so IDs are different for identical objects across both versions. Poof, all those won't synchronize. That may be stupid but it's easy, works and is not a problem as long as everyone plays on the same version. You'll easily find tons of things that were built on similar assumptions for the sake of simplicity.
Second, detecting each version used in a multiplayer game and merging the differences isn't something that's usually done in game engines, simply because it's several orders of magnitude more complex than just forcing all players to play on the same version. Playing on the same version requires a single check. Conciliating differences requires individually tagging all the content that would be different, overhauling all the loading code to check for such tags, and playtesting all the possible combinations to check nothing's being broken. If they hadn't planned from it, they aren't gonna add it now.