We ended the series with the Quelgrist Protocol(QP) out in the wild.
The genie was out of the bottle and this would eventually put an end to the Harlan family.

But, um, how exactly?

So, the Harlans were First Family, not because they're at the top of the ladder, but because they founded the colonisation and were their first.
Are we to understand that, in the hundreds of years they've been on the World, that they've never altered their genome, individually or collectively?

All the Harlans would have to do, to survive the QP is to stay in isolation, only allowing in serving staff in synth or grown sleeves, until they could have a set of sleeves grown that were free of whatever triggered those infected with the QP.
Or they could simply immediately sleeve into fresh, off the rack grown sleeves (probably cosmetically modifying them to look like Harlans.
They could also "offer" all high ranking officials, new custom QP immune sleeves, or make such a prerequisite for advancement.
And these could all possibly be temporary measures until they find a way to undo the QP contagion itself. After which the pull out some original Harlan sleeves from the same type of storage as Kovacs' vintage Eishundo.

The fact that this isn't really considered is either a plot hole, or it says something about their attitudes regarding, identity, neurology, or genes, and sleeving.
I'm not sure if it's legalities, or taboos/mores/customs, or neuropsychology behind the attitude(s).

Is the bias that growing altered sleeves to remove the QP triggering gene(s) would make the bodies not Harlans?
Is this a familial or cultural bias?

What does this imply about social conventions regarding the off-spring of people in grown/custom sleeves?
You and I have a child, and one or both of us is/are in custom sleeves. The resultant child would not have the familial genes of one or both of our families.
Is that child still considered a Jesus or a <insert your family name>?
Is this just a social more? Or does it also effect inheritance law?
Would it be that our child can be the default inheritor of its parents, but has no legal inheritance claim (or a lesser claim when genetic offspring exist)to the grandparents estates?

Morgan never really discusses procreation. Do people keep their genome on file or physical storage for such purposes?
If you had the baby made from gene stock, or eggs, would the mother in the foreign sleeve still go baby crazy for a child that is not genetically (to the sleeve) theirs?

Does this bias somehow tacitly admit that placing a stack (a mind) in a different sleeve, or anything but an exact clone, means that the mind will be, or have been, changed?

Either being digitally freighted means that the mind always exists on and operates from the stack, a step removed from the sleeve (in which case it now exists on a substrate which is much more immutable than a brain, and where creation of pathways can only mimic neurology), or...

That the mind is transferred to exist/operate in/in the new brain, via the cortical stack.
In which case, while it doesn't have the issue of merely imitating neurological function, it is still a significantly different substrate, and the brain will alter the mind.
Anyone who has been on an antidepressant, or other psychoactive medication, has experienced how sensitive our minds are in relation to minute changes in chemical balance.
People who are examples of neurodiversity, or suffered from neurologically based "disorders" or damage and have received treatment that has changed their quality of life, eventually question their own identity and whether or not they would be "them" if they were (more) neurotypical.

The fact is that separating the mind from the substrate, without affecting the mind, cannot be done.

This is barely given any light in the books. He mentions the scent based emotional attachment to Ortega, but that's pretty much it.
Perhaps part of Envoy conditioning is aimed at making Envoy minds less mutable and able to deal with such changes. But even so, long term use of a sleeve should have a permanent effect (until the next sleeve).