So, I have spare 13" MBP (2013) that contains nothing but a clean install of El Cap (i.e., no additional apps or software beyond what is included in a clean install).
I did the upgrade to Sierra. Took a while, but no problem. Using my other 13" MBP (2015) which has the ScanSnap software, I used a USB drive to move a few pdf files created using ScanSnap (they are actually scans of car repair receipts). None of the files had OCR performed on them at the time of scanning, nor did they have OCR performed on them using any other software. In other words, they were just scans. Once on the new Sierra machine, and using Preview, I open each, re-saved, opened again, put rectangles and circles all over them (couldn't highlight text because, as I say, they were not OCRed), and re-saved and re-opened again. No problems with any of them. No corruption, no blank files, etc.
I went back to my main 2015 13" MBP running El Cap and did a fresh scan of a letter and had the ScanSnap software OCR it as part of the scan process before saving it as a .pdf. Using the same USB drive, I moved the new file over to the Sierra machine. Using Preview again, I opened it, underlined text, selected text and highlighted it, re-saved, opened, highlighted more text, did a strike through of other text, re-saved it, and re-opened. No problems.
I still may hold off on installing Sierra, but at least this gives a bit of first-hand data/experience to the issue.