OCR removes annotations from PDF files

I am a researcher and have hundreds of PDF files, most of them annotated using Acrobat 8, DevonThink and Preview.app. Annotations include rectangles, some highlighted text, arrows, “typewriter” text, and notes.

Yesterday I set out to make these PDFs searchable. To my dismay, however, I soon realized that the resulting files do not contain any of my annotations.

Is it possible to perform OCR without sacrificing the annotations? Would you perhaps know alternative software solutions to this end?

Thank you very much.

UPDATE: One solution would be to “flatten” the PDFs before feeding them into DTPO, but I am not aware of any way to batch-flatten hundreds of PDFs!

DEVONthink Pro Office can’t do this (yet), therefore it’s recommended to OCR the documents first.

Maybe Acrobat’s OCR?

You could try the script posted in this thread: viewtopic.php?f=20&t=6966

Thank you for the suggestion. Indeed, Acrobat 8 Pro does the trick, though I was hoping to benefit from Abbyy’s putatively higher accuracy. Much better than nothing at any rate!