I have a strange one. I have an InDesign document that was created years ago. Our company went through a rebrand so I revamped the entire thing, new layout and new color scheme. The graphics are all graphs that are linked from Illustrator documents. They were updated to the new color scheme. The problem is that in both Illustrator and InDesign they are appearing with the correct color scheme, when I "Save as a PDF" the old color scheme appears.
In InDesign the old colors are showing as swatches that can not be deleted. When I try to find in the document they are listed as in the Illustrator files. I reopen in Illustrator and see absolutely no sign of the color in either the illustration or in the swatches. I have tried copying the Illustrator files into new illustrator documents with new names, they still hold the old color scheme. Any help in trying to get rid of an old color scheme? I feel like there is a setting or tool that I am not familiar with that just needs to be messed with to fix. This one is stumping me.