Highlighting in Devonthink removes OCR?

I imported a bunch of TIF files into Devonthink today and converted them to searchable PDFs. Then I went through them and highlighted portions (still in Devonthink). Each time I highlighted something, that file lost the OCR.

Is this connected to the Sierra PDF/OCR issues?

Yes. It is exaclty the issue in 10.12.2. Our Lead Developer has noted the most recent beta of Sierra is not exhibiting this issue, so we are hopeful it will be fixed in the next OS release. However, we are still going to be issuing another maintenance release as well, so stay tuned for that too.