I know the situation you're talking about.
I'm pretty sure you will be able to transfer- I've seen Dukes that are not regional Lords before. However, as a Duke you cannot take an estate without being a Lord, since that would make the Duke a vassal to another Lord and thus break the chain of command. So to accomplish what you want, you would have to 1. step down, 2. appoint yourself as Lord of the vacant region, then 3. claim an estate in that region.
I don't think you will be removed as Duke if you step down as Lord. There are even Duchies that do not have a single region in them, and yet their Dukes still retain their titles.
I hope this helps.