The recommendation comes from TidBITS publisher Adam Engst. Writing on the online Apple newsletter website, Engst backs up fellow developer Craig Landrup's claim that Apple's decision to rewrite the PDFKit framework for macOS 10.12 has broken basic functionality that PDF-related developers rely on, such as compatibility with ScanSnap and Doxie scanners.
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.As to why issues have arisen in Apple's native Preview application, Engst quotes approvingly the DEVONthink developer Christian Grunenberg, who characterizes the rewritten version of PDFKit in Sierra as a "work in progress":
Apple wants to use a common foundation for both iOS and macOS. However, it was released way too early, and for the first time (at least in my experience) Apple deprecated several features without caring about compatibility. And to make things worse, lots of former features are now broken or not implemented at all, meaning that we had to add lots of workarounds or implement stuff on our own. And there’s still work left to be done.Apple previously removed functionality in its iWork suite for Mac to conform with iOS, but re-introduced most of the missing features in a later version. Whether Apple plans to do the same with an update to Preview is still unclear. Meanwhile, until Apple fixes the issues with the native Mac app, Engst recommends Smile's PDFpen as an alternative for PDF manipulation of all sorts, with Adobe’s Acrobat DC being a more expensive option.
10.12.2 introduces new issues (it seems that Apple wants to fix at least the broken compatibility now) and of course fixed almost none of the other issues. It’s not only DEVONthink — a lot of other applications (such as EndNote, Skim, Bookends, and EagleFiler) are also affected.