The control can't, but it REALLY can't because the serial protocol they use doesn't allow it.
What it does however is it adds the % character at the beginning and end of each file, just as you need to have those in there when you send them up.
That is the separator.
What you can use is NcPlot to bring in the gigantic file and then tell it to Save-As_separate, which will use the % character and saves the files individually by the Onnnn number.
If that is what you're after, then NcPlot is all you need.
Unfortunately the Onnn number filenames are quite useless on the PC so you might still have to go back and then rename them to something meaningful.