I have experienced problems with scanned PDF files after they have been edited with Preview. The post-Preview-edited files are corrupted in that the OCR layer is gone, and in some cases certain pages of the PDF documents are blank or gone.
Not all PDF files are corrupted in this manner. In my case, only the OCR'd files created with my Fujitsu ScanSnap scanner were corrupted by Preview under macOS Sierra 10.12.2. Other PDF files downloaded from other sources (bills, bank statements, etc.) and subsequently edited with Preview were not affected. Other users, however, have reported significant problems with files that have nothing to do with Fujitsu ScanSnap scanners. See the full discussion thread in the link posted above (post#4).
This apparent Preview-related file corruption only happens in the macOS Sierra version of Preview. This does not happen under OS X 10.11 El Capitan. This is a serious problem - many people rely on these PDF files for business (real estate, legal, etc.) and for storage of important personal files.
The MacRumors blog post (link above, post #4) refers to a rewrite of PDFKit framework for macOS 10.12. This may be at the root of the problem.