I am receiving a lot of email lately from readers encountering PDF problems on the Mac. If that’s you, you’re not alone. Apparently with the release of macOS Sierra, Apple rewrote many of the PDFKit frameworks used in Preview and several other third party PDF applications. (This is why the Fujitsu ScanSnap took longer to become Sierra-friendly.)
The underlying problem is that Apple wants to use the same foundational PDF code for both macOS and iOS. Sierra is where they started implementing this. Unfortunately, in doing so, they broke much of the code PDF apps rely upon. It was a good idea hatched too early. Adam Angst did his usual bang-up job talking to developers about this over at TidBITS.
I spend most of my time working with PDFs in PDFpen, which largely does not rely on Apple’s frameworks and works fine. After getting all this email, however, I decided to use Preview for a few days to see how bad it is. It’s a mess. Preview cannot not display (or properly save) some of my form PDFs and seems to be wiping the OCR text layer out of previously OCR’d PDFs.
I fully expect this will get fixed but in the meantime, I'm sticking with PDFpen and I recommend you do the same.