Our good friend Adam Engst at TidBITS reports on the many problems users and third-party developers have run into with PDF support in macOS Sierra, even under the latest 10.12.2 update:
It pains me to say this, speaking as the co-author of “Take Control of Preview,” but I have to recommend that Sierra users avoid using Preview to edit PDF documents until Apple fixes these bugs. If editing a PDF in Preview in unavoidable, be sure to work only on a copy of the file and retain the original in case editing introduces corruption of any sort. Smile’s PDFpen is the obvious alternative for PDF manipulation of all sorts (and for documentation, we have “Take Control of PDFpen 8” too), although Adobe’s Acrobat DC is also an option, albeit an expensive one.
Native PDF support was one of the great features of macOS, but even as a user I’ve noticed increasingly inconsistent behavior and compatibility over the last few years. (One issue I regularly have: form-fillable PDFs on the Mac often seem to lose their data when I send them to PC, requiring a workaround.)