Sound like a mess. Well, you can either patch it, or rewrite it from scratch, or walk away. Are you under the gun? In other words, are you being asked to do this in about 3 days when it would take a non-Greek god about 3 weeks to do? Your best bet is to implement a
state machine. The state machine will allow you to decide which state to go to based on certain events, and allow you to ignore events if you're in a particular state. You can create a state machine using the template that ships with LabVIEW.