No need to investigate, found the issue.
It seems that if you press "New game" immediately after "end credits", it keeps all affection levels. Strange as fuck, but there you have it.
So I played game with Skylar route, finished it, pressed new game immediately at ending and that loaded new game with high affection scores. Knew something was strange when I checked phone and saw character bios reference events that didn't happen yet in that playthrough.
For reference, no mods involved so it was just bizarre case
![Smile :) :)](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
P.S. Love the game and thank you very much for making it!