Old color scheme appearing in PDF

[Amy La Russa]

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.

[Amy La Russa]

update: I just tried saving an illustration as a PDF to link in the InDesign. The PDF opens as the correct color scheme but when put into InDesign and PDFed the old colors still appear.

[Monika Gause]

Are you overwriting the old file?

are we talking about two files? The AI file and a PDF? Or just one file that has both?

Where are you saving? On a network?

Can you try and disable the "Save in background" setting in the Preferences.

Then save the file not overwriting the old file, but creating a new one.

Here's how Illustrator files work:

https://youtu.be/IpDh8Y7q8yE

[Amy La Russa]

I found a solution. If I export as TIFs the correct color appears. I would still love to know how to fix the issue since my solution is just a workaround and not really a fix.