This will depend on the barfeed being used. In most cases the machine waits for an end of bar signal from the barfeed, then executes a sub-program that changes the bar, then returns to the main program and re-starts the machine. If you are trying to learn about this thing and never had any CNC Swiss experience, well.....lets say it can be done, but it might take quite a bit of time to figure it all out. All the Citizen books I have seen are written in Japenglish and should be translated. You may not be a newbie to programming, but Swiss machines are quite a different animal, as you are no doubt finding out.
As far as the alarm, Citizen has a list of alarms that are not included in the books for some reason. Unless you find someone who has had this come up before, you might have to call Citizen and ask a field tech.