I don't recall seeing this when I update versions, but I update links by reflex when I see the message so perhaps I missed it. You are going to want to update the links at some point so that you are using the latest versions of the linked graphics, or relink back to the old ones. Go ahead and update the Links as you open, or if you are more cautious, say Don't Update Links, and then do it manually through the Links panel.
Thanks, I have already updated to the old links for all files. However, I would like to know why this is happening and if there is a way to fix it. It's time consuming to update links, especially when haven't changed. I don't understand why my links are missing in the first place.
InDesign thinks the files were modified—perhaps there was time stamp update on your drive that doesn't match the time stamp that InDesign is using. I just created a doc in CS6, added a linked image, saved and closed it. When I opened the same file in CC 2015.3 it did not prompt me to update links.
I'm not convinced it's that time-consuming: when you open a legacy file, just click on Update Links when prompted. It's a single extra click.
Did I address the right question?
In the OP you said you had to update the files, which assumes they were modified but still in the same location. That's a single click to update. If they are missing, that's a different answer. Which is it: relinking missing files or updating modified files?
why my links are missing in the first place.
If they are actually missing, see http://indesignsecrets.com/fastest-find-missing-links.php . (Still valid for CC 2015)
Relinking missing files. Although, I get a message that the links have been modified, but they haven't.
The files are in the exact same location and have not been modified since the last time the documents were opened, so they shouldn't have to relink when I reopen the document. It is not a time stamp issue, the times and dates are correct.
It is time-consuming when you have to wait for 60+ files to update when opening a single document.
Ok, so perhaps the second link will be helpful (fasted find missing links from InDesign Secrets) if it happens with any other files.
And yes, the click to update is easy—but the waiting would be frustrating.