This doesn't completely fix your issue, but since you mentioned deskewing, I clean up my scanned documents using ScanTailor Advanced: https://github.com/4lex4/

This doesn't completely fix your issue, but since you mentioned deskewing, I clean up my scanned documents using ScanTailor Advanced: https://github.com/4lex4/scantailor-advanced https://github.com/4lex4/scantailor-advanced I find the autodeskewing algorithm to work well, but it allows hand adjustment as well, which I like. As I've gotten better as using it, I've been able to get the size of my scanned documents down considerably by cleaning up the scans. This includes some old manuals. As far as the pdf encoding itself, I use both mutool, from mupdf, and qpdf. I just checked and it looks like while they both compress their streams, it may not have the same flexibility with Acrobat Pro. For me, I'll decompress, edit, and recompress streams on the files and that's been fine for my use. That said, if someone knows of a better tool for compressing streams in a PDF, I'd be interested to hear about it as well.