Your Current color settings honor CMYK profiles in linked content but profiles were set to be ignored when document was created

"Your Current color settings honor CMYK profiles in linked content but profiles were set to be ignored when document was created"
I keep receiving this message on my illustrator files. They are linked to a file in Indesign that when saved as a PDF prints the wrong colors. I have been trying to fix this for two days. I have look online for answer in forums and articles and nothing works i am completely burn out, lost and angry Please help. This is a Picture book project that can not to sent to the author in this condition.

Your Illustrator files have images linked in them?
THis message tells you that color management had been set up differently when you created the document. In color management settings you have the choice if color profiles in linked images are ignored (and Illustrator uses just the CMYK numbers) or if those profiles are honored (and Illustrator converts the CMYK numbers according to the image profile and your settings into the Illustrator document's color profile).
What makes the whole thing even more complicated is that you placed the thing into InDesign.
So there might be 4 different color profiles interacting with each other:
1. the linked image's profile
2. the AI document's color profile
3. the InDesign document's color profile
4. The export profile in InDesign.
Is your color management set up and synchronized in Photoshop, Illustrator and InDesign?
Is it possible to place the images directly in InDesign? That is: create vector content in Illustrator and have photos separately? Then combine them in Illustrator?
How do you know they print the wrong colors? Just seeing them on your monitor won't tell you, unless your system is correctly color calibrated.

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