Hi,
As you noted, it sounds like the issue is that the PDF has embedded JPEG2000 images. That error seems to be thrown by PDFBox, which is the library DSpace uses to index and create thumbnails from PDFs (by default).
That'd require rebuilding / redeploying DSpace to ensure these new dependencies are installed on your backend. I'm not sure if it'd work immediately after rebuilding, or if more changes would be needed. (As I've never tried this before and not yet seen this error.)
Or, alternatively, you could try to use the ImageMagick Media Filters, which can also create thumbnails from PDFs. In this situation you'd disable the default "PDFBox JPEG Thumbnail" filter and enable ImageMagick instead as described here:
https://wiki.lyrasis.org/display/DSDOC7x/ImageMagick+Media+Filters That PDF thumbnail converter might have an easier time with JPEG2000 images (I admit though that I haven't tested it).
Tim