YoshiP said during a Q&A within the last couple of years that the housing system memory isn't designed to allow those sorts of changes/upgrades to housing that players already own.

What would be nice is if they expanded the apartment system to have such layouts as purchase options in the first place. Go to buy an apartment, you choose from several preset size/layouts. If at some time in the future the player decides they want a different size/layout, players could relinquish the existing apartment and purchase a new one with the new layout desired.