SPOILERS....
Sydney won't join you but will come after you later in the game if you got her love scene in CH16 and she has 10+ like.
Alice's stats vanishing may be an issue with the persistence file, because once you unlock it, it should ALWAYS be available, even with a new game. If you can access developer mode, you should be able to put in persistent.parttwo_end = True to unlock it.
Yeah I continued the game and she rejoined. I have played several VNs, but this game is insane! On one hand I want to see the end, but on the other hand I want it to continue because you actually get attached to all the girls and the MC. I am now waiting for the final release and want to buy it as a sign of support.