Originally Posted by dwanthny
He's not disagreeing with this theory. He is however saying that the process calibre uses to add metadata causes this pdf file to be changed in such a way that even Adobe acrobat is no longer able to open the full file.
I realized that. He was reporting that Reader 9 (software that supports Portfolio) would not read it, so I thought it was worthwhile to confirm that it's a portfolio format pdf problem, and not something else. A portfolio problem seemed the most likely, but not the only possible problem. He's got the original file and I'd start by looking at properties of that file in Reader 9. Maybe it will tell him.
As to how to flatten it, Acrobat Pro is the only method I'm aware of. There's a 30 day free trial available (Windows).