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I looked into this further and it calls jbig2-imageio to process any PDFs that are/have jbig2 format within them. I am not sure what changed between the versions, but I was able to get it to work by running Ubooquity with 'java -cp Ubooquity.jar:jbig2-imageio-3.0.4.jar com.ubooquity.Launcher --headless --remoteadmin'.
Maybe either the rewrite to kotlin or the pdfbox upgrade? Idk, just sharing what I have.