Yep, got an idea, but explaining it might be beyond my capabilities.
If that is a vector file, it’s going to have to do with how the Compound Path was created at that point…it’s a relatively complex series of shapes subtracted from the background, and you pretty much have to take it in stages to ensure that everything “punches out” of the background correctly.
In Illustrator, if you want to punch out a group of shapes that are not touching, you have to combine them into a Compound Path before subtracting them from the background. Also make sure that you turn on the background grid, so that you can see if there is a white fill shape on top of the background, or if they have all legitimately punched through.
It is generally much easier to just turn the QR code into a raster image in Illustrator (or Bitmap Copy in Inkscape), then it will engrave without any further modification. And it will be a lot quicker…
NOT when you are trying to do that many of them. Each will come across as a separate Engrave. Just go ahead and fix the vector file. You’re caught between a rock and a hard place here. Might as well correct the file. It will speed up the processing time.
Since that was likely a lousy explanation, I reworked one of the codes from your file…you can just copy and paste this one over the top of the originals, then delete the green ones to replace them.
plumeria_SWAG_WholeSheet revised QR code.zip (665.3 KB)