One thing that will instantly solve some of your issues: Duchy names are no longer bound to a region. That is, a Duchy may have any time, even if that name refers to no particular piece of land.
My character on Atamara is Duke of Sigrid's Mace; no such land exists. The only real tie Duchies have to land now is that they must originally be formed from a few specific types of regions and receive taxes for any lands included in it. It's even possible for a Duchy to exist without regions, but at that point it becomes just a title. (For this to happen, it must be formed from a region and then have that region leave the Duchy.)
As a side note, I'm still waiting for someone with a Theocracy to make Duke titles with no lands, but relevant to their religion... "Duke of Justice" or something, you know?
As far as the capital leaving, again, it's the Duchy leaving, not the specific land. I believe the Duchy would take any lands under it, though, so I wonder if the capital conflicted with that rule and now resides under a different Duchy, still within Sint?