Hi,
I don't believe it's possible to stop a stacked sequence structure once it starts running, at least not efficiently.
There is a structure that's recommended for this type of application called a state machine. With a state machine you can programmatically determine which state runs next. A state would correspond to a sequence in your stacked sequence structure.
You can have a look at the form a state machine takes by opening a new VI and choosing "New..." from the file menu or "More..." from the (lv8) splash screen. This will open the New dialog box. Browse to VI >> From Template >> Frameworks >> Design Patterns >> Standard State Machine.
A different state of the state machine executes for each iteration of the while loop. The shift register with the eumerated constant determines the next state to run.
The following tutorial has more information on why you would use a state machine and how to build them:
http://zone.ni.com/devzone/conceptd.nsf/webmain/c74cec177a289dbd86256c4e00600196
Let me know if you'd like more information on this.
Kind regards
Sarah
Applications Engineer | National Instruments | UK & Ireland