I'm not having CTDs or anything, but I'm also in the process of remodding the five original player homes for use with HF installed and I'd like to arrange things so that I don't lose alchemy and enchanting tables, etc. when I get the child's bedroom decorations from the steward for those houses.
What actually controls the disabling of the affected objects when the child's furnishings are purchased? I can see that some of them appear to be linked up to something now that wasn't there without the changes made by the DLC, but this doesn't seem to be the case with everything as far as I can tell. Or else I'm underestimating the number of vanilla items that get disabled when the child's furnishings are purchased.
Is there something else in the CK or a script that causes those things to be removed? Like, something that tells the game to just get rid of an entire room's previous decor, without respect to what I can see when I edit the individual items in the CK?