Sorry for the delayed response. I haven't been able to check the Forum for a while, and I had to find some time to work this one out.
If you still want a solution for this, then the answer to your question is yes, you can crop a Zoomed Area, to make a new Reference Waveform. You can do this using a Math Channel, that I created, as follows:
( ( sign( -( T - Zoomed Area Start Time )( T - Zoomed Area Finish Time ) ) * Channel ) + Channel ) / 2
So, what you need to do is,
(1) Position the Time rulers to the Start and End of the zoomed area and make a note of the start and end times that are shown in the 'Rulers' box, in seconds, including the polarity (e.g., -0.0047 for -4.7ms).
(2) Create a new Math Channel and copy the Math Channel formula, above, into it.
(3) Copy and paste the values, that you made a note of, into the Math Channel place holders for the Zoomed Area, and enter the Channel letter for the data that you want into the 2 other place holders.
(4) Complete the creation of the Math Channel, and then create the Reference Waveform by selecting the Math Channel you just created.
There is also a GIF file showing these steps here: .
1/ You can easily position the rulers by moving the first one as far as it will go, to place it at the end of the Zoomed area, and then just clicking on the second ruler (without moving it) to place it at the Start of the zoomed Area).
2/ In the GIF file I am detaching the Notes window, so that I can switch context to and from the Notes Window, to cut and paste the time values using Alt-tab, while the Math Channel creation window is still open.
UPDATE - Sorry forgot to add the data file, so that you can check the results: