I have an InDesign file that I received from a client, when I open the file from a package I am told that links are missing. In comparing the "missing link" location and the "modified/fixed" link locations the location is exactly the same, but InDesign no longer thinks the link is missing. Does anyone have any ideas as to why this could happen?
It sounds like a fluke to me, and hopefully fairly easy to relink the missing files, so I wouldn't worry about it too much. What's really odd about this, however, is that you shouldn't be getting the "modified/fixed" error message either assuming you haven't moved the InDesign file out of the folder that also contains the "Links" folder.
But, if I had to guess, I would lay odds that this is what happened. Whoever put together the original InDesign document packaged it, and then started changing the files in the packaged Links folder. Maybe they decided to replace a bunch of images with higher resolution versions before they sent them to you. If the name of the higher resolution image was the same as the one that was originally created by packaging, InDesign will show you that the link was modified. For the images that show up as "missing," maybe the original user decided to change the name of the images in the links file so that you would be able to better identify each of the images by their file name. If so, InDesign is going to show that those images are missing.
You might be able to get a hint about what happened by opening the "Link Info" drop down in your links panel. Take a look at the path that is shown at the bottom of this panel, and see what it shows for the original path and/or the original name of the missing linked file. That may well give you the clue to figure out what happened.