The more I look at your program, the less I understand it.
Why are you setting number = number in a case if SO2 = ""? number always equals number.
In your sequence frames 1 and 4, you have no control over which write (date or time) happens first. Just placing one function to the left of another doesn't make it happen first if your wiring doesn't create data dependency. Review the section on Data Dependency in chapter 5 of the LabView User's Manual.
It looks you're writing to and reading from the same file using Write File and Read Lines from File.vi. Why read back data you just wrote? You have the data on your diagram. If you want to convert it from string to numeric, use a Sring/Number Conversion function from the String palette.
On Read Lines from File.vi (which I'm not sure you even need), you should use a shift register for the start of read offset rather than a local variable for mark after read (chars.). With a shift register, you can initialize it to 0 when the VI starts. Using a local, if you restart the VI, it will try to startup from where you left off the last time, but you just opened the file for create or replace.
In your sequence frames 2 and 3, why do you wait for the number to be less than the numeric before writing a carriage return to the file? Also, LabView has a End of Line constant which adapts to the expected value for the operating system. That's generally more flexible than a Carriage Return.
It looks to me like you're overusing control refnums. You don't need to use a control refnum and a property node to set or read a control's value if you can wire directly to the control's terminal.
I really don't understand what you're doing with pause and variants. I may be missing the point, but it looks like you made this much more complicated than it needs to be. Why not keep it a boolean?
For your pause-path, you open the file but never close it. You can lose data that way. You also open it using open function 3, create new file. You'll get an error if the file already exists.
On a general note, your diagram would be easier to read if you were more selective in how you routed your wires: you have wires on top of wires, wires running under sub-VIs, wires running in the frame of a while loop, wires running under labels.
I think there's a temptation to overuse sequences. I don't think you need one here. As I mentioned in my earlier message, case structures and shift registers will be more useful to you.
