Yes, it would. Each island has island-specific region numbers--meaning that there is a region #1 on every continent. So your brave new would would require renumbering every-single-region. And then redoing the mapping between every-single-region and their neighbors. And then adding the sea zones, ferry routes, and the routes between worlds. It would take forever.
Also, it's possible to have a "Bob" on Atamara, and a "Bob" on FEI, and a "Bob" on EC. You'd have character name collisions--which character gets to keep their name, and which has to change their name?
And then, how do you deal with the judge "deport" option? Are you going to make is to their only option is to execute banned nobles? Or are you going to keep the Colonies separate, due to the one-turn-a-day, so that everyone deports to the Colonies?
I don't think the numbering and pathing is such a serious issue. Add a digit as a continental identifier, and voilà. There wouldn't be any more ferry routes, and sea zones don't look overly complicated to code.
What I think would take more time would be to recode stuff that were continent-specific, like number of character or title restrictions. New code could simulate in a fairly straightforward way, I think, but coding it might take some effort.
Your suggestion for deportation actually sounds good. Keep the colonies apart, merging it with two-turn continents wouldn't seem ideal. An alternative would be to quite simply mimic the current system: your actually deport a character to another island, despite it now being all in the same game world. If he wants to come back, he'll have to sail back.
Overall, I think there's plenty of solutions possible. Most of the work would likely go into adapting those mechanics, though, but the net gain would be suddenly granting everyone a whole bunch of new neighbors to interact with.
