I read about the "not deleting vanilla objects" thing and so I decided to give it a try.
I made a new mod and didn't delete a single vanilla object - recycled EVERYTHING - even the roombounds and portals, yes even the navmesh. It was the kind of work to drive you into insanity.
And guess what...
CTD!

So that was it for me - I'm done with modding Skyrim - at least until one of the "gods in greasy T-Shirts" aka game developers (instead of"gods in white"

) may give us the - unearned - honor to adress that problem and offer some kind of solution, or at least a technique we might be able to track the bug with.
Good luck to all of you

.
Perhaps my next try will be just cloning the cell and basically linking the doors to lead in/out of that cell.
Well - that is not that easy. You have all the x-markers for house-decoration. So you will have to move them to the new cell and then edit all references to them in scrips and quests. And possibly there may be other users of the respective cell name too (other scripts, quests, dialogues whatever) - probably an immense source for creating new bugs...

IMHO in the current state the Creation Kit is insufficient to edit player homes in a significant scope...a pity...