This is a weird problem I just encountered after upgrading to 2.1. I don’t know if it is at all related to this version.
I have downloaded a number of pdfs for incorporation into Papers. I can OCR most of them without difficulty, if they aren’t already in that format.
However, I found two papers that would have all the text missing from selected pages after OCR. It seems that any page with just text would become blank after OCR, while the pages with an image on them (a radiological image), would OCR fine.
If it helps at all, when I opened the original pdf in Preview, and then tried to delete only the page with the image, it wouldn’t work. If I copy all pages, print to a new pdf, then open the new pdf, I can then delete the pages with images on them.
So I can just mix and match two different versions, and get successful OCR on each, and then merge. Then, the pages with images are smaller, but at least I have an OCR’ed pdf.