Brooks Duncan performed several tests to confirm that Preview on macOS Sierra 12.12.2 destroys the OCR text layer of certain PDFs.
I’ve been extremely happy with PDF Expert as my default PDF app for macOS. I promoted it to my primary PDF app soon after upgrading to Sierra because I noticed that Preview would also break the internal table of contents structure of PDFs.
I never thought I’d see the day when I couldn’t even trust something as basic as a PDF to Apple’s software. The new PDFkit stuff in Sierra should be an embarrassment to Apple. PDF support should just work.