In the last couple weeks my InDesign CC 2015 is having trouble with links. Every so often when I go to sane a file I created, I have to save as. When I do that it breaks all of my links. I also am having trouble copy/paste or move a page to a new document without breaking all of the links. I work on network drives on a Mac running Yosemite and CC 2015. I have not updated anything in the last couple weeks since this has started happening.
Does anybody know what is happening? Re-linking hundreds of images is very time consuming as the images are everywhere.
Try trashing the prefs. See Replace Your Preferences
You might want to do a test on a copy of the file so you don't lose the links while you're testing. It might also be worth testing when logged in with a different user account before trashing the prefs. If it doesn't work in the new account, it's not likely to be solved replacing the prefs, but it may be telling you you have a conflict with other software that's running.