When saving into a PDF file larger than 225.5417" it uses the new extra large artboard feature (since version 24.2). This applies a scaling factor of 10 so that the file can be viewed properly in Acrobat.

The issue is that if you downsample your images it doesn't take into account the scaling factor. This means for a 1000" document, if I want to downsample to 300 dpi/in, I will need 300 000 dpi. But, the downsampling tools views the document as being 100" instead, and I end up with 30 000 dpi. So the end result is a 30dpi/in image.