In your example there shouldn’t be any change in my opinion.

The sentence you provided becomes in negation: Je n’habites pas dans une jolie maison.

There is a possibility for a change here but you need to double check:

J’ai une jolie maison -> je n’ai pas de jolie maison

What changes for sure is ‘des’. It changes to ‘de’ when it precedes a descriptive adjective – Adjectif qualificatif.

Example:

Elle a DES cheveux becomes elle a DE beaux cheveux

Il donne DES conseils becomes il donne de bons conseils

I hope this helps.

https://www.francaisfacile.com/exercices/exercice-francais-2/exercice-francais-24927.php

You want the negation of the sentence “J’habite dans une jolie maison”. Obviously the negation is not “Je n’habite pas dans une jolie maison” but

“La maison dans laquelle j’habite n’est pas une jolie maison “.

It is indeed clear that the emphasis in the first sentence is about the qualification of your house as “jolie” (nice), thus if you want to negate that very sentence, you should put the negation on that qualification. Of course, you do not want to say that you do not live anywhere, but that the place in which you live turns out (maybe) to be fine but not nice.