Boy, do I miss Prinergy!

Just tested it. Remap to Separation works. 

Yup. Convert to spot would probably work best. Or you could remap to a different channel. 

Another option to think about is to use the same procedure but change the color (but dobt delete) of whatever is going to be deleted. Change it to Magenta or something that stands out. Then you run the that first so you can easily scroll through the entire document and see what changes colors - that's what will be deleted when you do the real thing.

My thought was there's probably not much important stuff in the corner so less likely to have design elements go along for the ride. 

I might be oversimplifying, but I took your sample file and viewed it in wireframe mode to see the underlying structure of the elements. On these 2 pages the die image is pretty close to the top left edge of the page.

So, I did Select Region of .25x.25 of the top left corner, anything fully enclosed or overlapping, then Remove Selection. Worked on these 2 pages.

Maybe you need to see what the variation is across the pages and try to make the region the smallest it can be but still safely get the dieline image.

If the die is an image, you can select only images in the region and delete them. 

Otherwise, as previously mentioned, you can select by color if the die is a spot. 

Neither do I. Sometimes there's something running under it that might look weird. Usually in those cases I'll use a rich black but it's not always necessary. 

-redacted-

That works, too, just a lot of extra steps to remember every time which means opportunities for mistakes. For me, the advantage of defining special colors in the rip is that you only have to define the color in InDesign as a spot and be sure it is named correctly - nothing else matters. And configure your rip so it by default checks the custom library first when it is handling spot colors. The properties defined in the rip will override any settings you may have applied or not applied in the source file. 

I make sure in the rip I define all the possible ways a die color might be named - DIE, die, Die, Dieline, DIELINE, dieline, etc. You can also add variations for Fold, Perf, whatever you need. 
 

Not used XMF, but in its color library where you define how to treat the color are there options like Transparent or Dieline? Prinergy and Prinect let you define that and it informs the rip how to handle it. Classifying as dieline means it always overprints, never plates, and allows colors underneath to trap to each other. 

Looks like half our jobs 

Lots of great ideas are born out of my laziness!

I would copy all the info and paste into a text editor. Then once the QR code dialog is open, you can leave it open while you go to the open text document to copy the next bit, then return to ID to paste. 

Or, duplicate the ID file and switch between documents (might not work but worth a shot)

At my old shop if all the fields were wrapped with quotes an empty value showed as ,"",