So I've got the newest version of this game. however, I can't get past the Halloween special. Whenever I and Hugo are going back on the train after defeating Wingo it ends and says see you in the next update. However, there's been a new update already so what do I do? I don't really want to restart the whole game again if possible. 

The end of the Halloween events for all characters is currently the stopping point in the game.
You can reload a past save, and see if the next part will be flagged for you now, and let you go onto the next part of the main story.
No need to start the entire game over again, but the best save point to hold onto, is after the Fury fight in the church, when Wolfstar is alone in his room and getting phone calls.  This is actually how you can see every branch of the game thus far.