Can any of your apps batch OCR PDFs?
I'm not going to guarantee the quality of Nitro's OCR, because I haven't used the product since they bought it from Smile.
I did just run a test with the current version and wasn't fully satisfied with its ability to detect whether a PDF needed to be OCR'd.
Try running this macro on a couple or three of your non-ocr'd files:
If you get what I expect I can probably write you a macro to do the testing.