That depends how far we go with this, once the technology is there to mix in 'healthy' genes with deleterious ones the door is immediately open to add genes from a 'library' as well.
Say a couple want children, but they want a red-haired girl, even though their genetic combinations make that an impossibility (just for the sake of an example I took something from the 'cosmetics' department, not from the disease department) you could conceivably splice in the genes to make that happen.
The problem here is that even though the resulting phenotype may be the desired one that there could be any number of interactions between the 'undesired' genes and the rest of the genome to keep the genome as a whole stable across generations.
It will take a long time before we will know if that's the case or not.
to keep the genome as a whole stable across generations
Why would you want that, if every generation has the option of designing their children anyway? And they can always revert to a backup genotype from 2000 if there's no other recourse.
Ordinary natural selection, including human sexual selection, works this way too. I still fail to see why you worry.