I have the same problem, with the very first upgrade and realized it after 6h of gameplay in HoS (started a NG+ few weeks ago) so no savegame were available. I tried to upgrade further, with the bed and the stable. It works for the stable (but still no grindstone, armor table and secret room in cellar), but it didn't for the bed (it looks like the skin is upgraded but there is no sleeping bonus). The I rollbacked before these second upgrade and I'll wait for the fix.
I really hope it will be fix soon cos i'd like Corvo Bianco to be a part of my B&W experience.