Hmm I'm not sure how I can help, I've never had anything like that happened. I sometimes have an issue with odd roof/window raises but it's always due to the terrain level being off after CFE use.
Is rebuilding the castle from scratch an option? It must have taken a whole lot of time to build in the first place, but perhaps that's the way to go to ensure you objects don't keep sinking? Make sure you build it on the flattest surface possible and with CFE cheats off completely (unless needed for building something) to attempt to avoid the sinking bug.
I can't really tell what's going on exactly from the screenshot and I'd offer to look at it in my game but I do not have DV so half of the objects would disappear.
