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I was sent a PDF that when I open it on Illustrator, it inverts the colors on the image. The image is embedded, in the Links panel its say NA for format. The file was originally created in Flexi, which I assume is the issue, I just want to know what and why. My solution was to simply invert them back. Here what's weird... The thumbnail preview in Finder display the color correctly, it's when I open it on Illustrator that they get inverted. Tried Photoshop, same thing, preview displays as it should, when opened it inverts them. If I open it as a PDF in Reader, it displays just fine.
The answer to your question is simple. Opening PDFs in Illustrator that were created in other applications can cause strange things to happen. Why? Illustrator is NOT a PDF editor. If you want to edit a PDF, try the editing features in Acrobat DC.
Here's a video tutorial about these features: http://www.jeffwitchel.net/2015/08/edit-pdfs-like-never-before-in-acrobat-dc/
Enjoy!
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for what its worth, in the past i used to get inverted jpgs from illustrator export. apparentlly this happened when document was set up with a cmyk profile instead or rgb one. once i converted to rgb all exports where normal. (illustrator did not have convert to srgb like PS had in the jpg export dialogue)