I believe I've seen this before where when you saved those sims, the save also registered that they already had parents who are no longer existing but at the same time they did at one point and so you can't fill their spots with someone else bc they did technically exist to create the children in the first place.
I remember that one time I created this household where there was this lone grandmother who takes care of her only grandson and their pet cat. I remembered that I couldn't register the grandmother as the teen's grandmother without having made a parent to then have the child that would be the teen grandson. I did this all in CAS; create the grandmother, then create her daughter, then create the grandson from the daughter, then deleted the mother to register that she doesn't exist within the game. I let them play in live mode and that's that.
Sometime later I wanted to have this YA townie from one of my saves become the mother of the grandson, and tried to add her into CAS into their family. I was able to make her the daughter of the grandma, but could only keep her as an aunt of the grandson and couldn't force the game to register her as the teen's own mother bc technically she never was to begin with.
I did just test a workaround that if you saved both of them separated in your library, then go into a brand new CAS and re-add them both into one household, you can then make them their parents again. If that still doesn't work for you, I know there is a mod that can force the game to register them as their parents.