macOS 10.12 Sierra has been plagued with PDF problems. First, there were problems with PDFs created using ScanSnap scanners, but those issues turned out to be relatively mild and Apple addressed them in the 10.12.1 update.
Unfortunately, 10.12.2 Sierra ushered in even more troubling issues with PDFs. Developers have reported a number of PDFKit problems, most notably the OCR text layer being deleted when manipulated by apps using PDFKit, including Preview. The main takeaway is that you shouldn’t use Preview to edit PDFs until these issues are resolved, hopefully in 10.12.3. In the meantime, if you have to edit a PDF, either work only on a copy, just in case, or consider investing in Smile’s PDFpen, which annotates and edits PDFs independent of Apple’s PDFKit.
For more about this problem, read the TidBITS article Sierra PDF Problems Get Worse in 10.12.2.
[Fixed? In the release notes for the 10.12.3 Sierra update, which were made available on January 23rd, Apple says that the update “fixes an issue that prevented the searching of scanned PDF documents in Preview.” Other PDF-related problems appear to remain in Preview, so continue to work with caution even after you install this update. See Apple Releases macOS Sierra 10.12.3, iOS 10.2.1, tvOS 10.1.1, and watchOS 3.1.1, in TidBITS, for more information. —Tonya, 1/24/2017]