Linked files in Indesign, made in Illustrator and stored on CC, are not updating

I am working with Indesign and Illustrator documents stored on my computer and synced to Creative Cloud where coworkers can access them too. I thought I was all ready to go to press and had the final PDF made when I noticed the wrong coloration in all of my maps in the book, 15 of them. I went back to the Illustrator map files and figured out the problem was a white base layer I had put under my shaded reliefs, which I had set to 65% opacity. At one time in the process, I thought the white base layer would add more light to the image, but, in the end, it just altered the colors in a negative way. Anyway, that was an easy fix, just delete the layer, save the Illustrator file, and then relink it in InDesign. Right? Not. For some reason, not all 15 of the maps wanted to go back to the version without the white base layer. 11 of them did fine. I opened the Indesign file where those maps were linked into, and Indesign prompted me to update the link, and it brought in the map without the white background, hence the map with the better colors. On most of these updates, I got the following message:

It's a weird message that I have never gotten before when I have added or removed layers from maps and then updated them in Indesign, but it worked nonetheless. I just clicked ok and Indesign brought in the good map.

However, 4 of the maps would not update with the good map. I tried the update icon and the relink icon, and these four maps still had the old bad colors...even though I had deleted the white background layer in those four maps and saved them before trying to update/relink in Indesign.

What is going on? How could Indesign remember data that is no longer there? Why would it not update? I'm going to try again now after spending 15 minutes writing this post to see if maybe the changes hadn't been consummated in CC (although, all the files had green checkmarks when I was trying before). Here goes...Nope. Indesign will allow me to try (the buttons aren't grayed out), but it won't update to the newly saved Illustrator map files.