Which exact version number of Lightroom (x.y.z)?
Mac or Windows? Which version?
If you are running Windows, this problem is most usually caused by Windows changing the drive letter on you. You can fix this by using the Windows Disk Management tool to change the letter to what Lightroom is looking for. If you pick a drive letter L or bigger, Windows will stop changing the letters on you.
I'm using Lightroom CC 2015.10. I made sure it was all up to date this morning.
I tried to move the port the EHD was plugged into, to see if that was the issue. But the same error occurred each time. Would changing it manually with the Disk Management tool do something different?
Additionally, it doesn't even show them as missing in some cases - just nonexistant. For instance, I have a folder labeled 2016 and all of the months under it. It shows some of the months with the images present, some months with the images as missing and some months where the folder is just completely empty?
Thanks for your response ManiacJoe
The physical port the drive is plugged into makes no difference regarding drive letters. Manually changing the drive letter is required.
Since Lightroom is not a file manager, Lightroom will "know" about only the files you have imported. It will not "see" any other files.
If you have files that are no longer in the catalog that were previously in the catalog, you might check your /file/recent/ menu to see if they were imported into a different catalog.