Bugs in macOS Sierra's PDF framework are causing headaches, both for Preview users and third-party developers.
A bug in PDFKit in macOS Sierra, thought to have been finally fixed in macOS 10.12.1, has apparently re-emerged in macOS 10.12.2, the most recent public version. In particular, these bugs cause problems for those that edit PDFs in Preview, along with third-party apps that make use of Apple's PDFKit framework. In particular, the bugs appear to affect optical character recognition (OCR) in PDF documents.
More concerning, and this is what finally pushed me to track down all these reports and write this article, is that the recently released macOS 10.12.2 has introduced a serious new bug related to PDFKit. Brooks Duncan of the DocumentSnap site published a note from one of his readers that warns that the OCR text layer added to scanned PDFs by Fujitsu's ScanSnap software will be deleted if you edit the PDF in Preview.
The bugs originally cropped up in the fall with the release of macOS Sierra, and were thought at the time to affect PDFs created with Fujitsu's ScanSnap scanners. However, it now appears to be a more widespread issue. The major issue seems to be that Apple rewrote the PDFKit framework for Sierra, which seems to have broken a number of things that PDF apps rely on.
Apps using third-party PDF libraries seem to have escaped any issues directly, but there can still be issues that crop of in documents edited in Preview.
For the time being, there has been no comment from Apple on the issue. It remains to be seen if the bugs will be fixed in macOS 10.12.3, currently in beta testing.