Instances or not the game using exclusively the \\AppData\Local\LifePlay\Saved\ folder to store game state. So it is a shared folder for data (like character variables, stats, dependencies, map data, etc), and your instance's folders are for save your characters (as presets). I think there is a big chance to you can make a situation by this way (using 1 save for all) where the characters ids or they stored variables are not identical on the different playthrough and the datas being corrupted.Tested a bit more, played through a new save again only using your mods and a few base mods.
Started with only one family member played a few hours, established incest relationship which worked. Showed correctly as mom/girlfriend. Was able to add addional family members to the world after relationship was established and all worked fine.
Loaded save right before asking for realtionship from mom. Added a sister and an aunt. Asked mom for relationship she gets deleted right there. Specfically once she says yes and the slide transitions to contine date or sex right there the game blinks and they disapear from the room typically all other npcs disapear too from the room if your at the bar or something. However only the one relitive npc you asked for that relationship with gets deleted. I can still hit the continue date or sex right there but the continue date leaves you just standing there as if the date finished with no say goodbye. The sex option leaves you in a scene with yourself and a blank tab over where the arousal data is where the second person widget is displayed during the scene.
Like I said it could be something is braking on my end but I have set this up three diffrent installs using no other mods and this result always happends. Hope this info can be helpful.
Regardless, the error could also be in the scripts.