First, you shouldn’t delete vanilla references. You can and should move them way down below the cell you’re working on and set them to be initially disabled. Then you should remove the “enable parent” link in that tab. That way they cannot get enabled. Also, with havock items like plates and food, you might want to make sure they’re sitting on a solid surface even though they’re way below the actual interior. For my Breezehome tweaks mod, I turned off collision and flew down to where I moved my unwanted stuff to, and the havock objects were falling over and over and over. I pulled my mod back up in the CK and set them on the table and floor piece I moved and they’re fine now.
Secondly, if you are checking your changes with a save that previously had those references enabled in the save you will get those type of glitches. Your best bet is to pick up a save just before you purchased the house and go from there. Since those references were never enabled and saved in your save you shouldn't have any problems.