If you Right Click on each and select Show Parent Folder, what does it look like?
"Show Parent Folder" appears in the menu of the "ghost" folder only. When I right click on the regular folder, I do not get that option. In the attached image, the two folders I highlighted in red are the same folder.
The folder highlighted in yellow should appear in the green box. I hope this image will make this easier to understand.
I hope this message finds you. If you get a chance I'd appreciate your input. I replied to you yesterday and I was wondering if that might be useful to you in figuring out what the issue is.
What happens if you rightclick on the two 2013 folders and select show parent folder? I think you need to keep going up in the folder hierarchy until you get to the top folder. LR should then merge them IME.
I had this happen to me several times on LR 4.4 with the same version of OS X as you. The hard drive in question was an external NAS device which had some questionable interactions with the OS to begin with, but was basically usable. Unfortunately I never figured out exactly what triggered the problem, and I only have a fuzzy memory of how I resolved it.
I believe what I may have done is something along these lines (but again, I can't remember exactly)
1) Using the Finder, rename the folder. This causes it to go missing in LR and show a question mark icon.
2) In the LR folders panel went to the other, "main" copy of the hard drive, went to the parent folder, and used the "synchronize" command to find the folder. Or maybe I added the folder back some other way. I think this caused the folder to reappear in the "correct" copy of the hard drive, and for the extra copy to disappear.
3) Renamed the folder back to my original name.
Sorry I can't remember exactly what I did. All I know for sure is that I forced the folder into a missing state temporarily. The double/split HDD icons seem to be a bug of some kind. If I were a better citizen I would have reported it to Adobe at the time!
jtopaz, it worked!
I took the same steps as you described and it worked the way I'd hoped it would. Again, thank you and everyone else who helped, I really appreciate it!
I have what appears to be the same problem, in Lightroom 6.14.
Furthermore, if I select Show Parent Folder against one of the folders in the second "phantom" D drive, I get this error "An internal error has occurred: Database.... UNIQUE constraint failed". That's a relational database data integrity violation being flagged. It seems my catalog is corrupted. What are my options?