From the way I know some of these patches work, the character names should stay the same throughout the game because they are calling for the same variable Like the MCs name remains the same no matter the version. Info that occurs doing the incest wild thang in the new version must be updated to do the incest thang.
The other two ways of "secretly" setting up incest (or any other fetish that Patreon has said is bad for our mental health) are write both paths in the game code, one with no incest, and the other with incest. Now, to enable the incest route is had an added patch which sets up the flag to allow incest or setting up the relationship between the various character who may do the incent thang. Like if by default the relationship is the "mother" figure is listed as the Landlady or Step-mother. Change that to Mother, Mom, etc. If the dev added the name you chose the incest is working.
Not keen on the relationship route though. The list of potential relationship names will be large, sorta. Like here in the US mother or mom is the default way, but what if you want to use mama, mum, (japanese: okaasan, okaasama, haha), (german: mutter), etc.
Ok. The relationship route isn't that big a problem.