I recently had a permissions problem with LR and followed Adobe's steps to correct it. Now LR sees 2 drives where there is only one- it lists 2 identical drives under the Folders section but with photo folders divided between the 2 "separate" drives. I tried dragging the entire folder and library catalog to another drive but LR will not reassemble or perceive all of my images.
Jim Wilde has provided an answer for a similar "phantom" drive problem-
I sounds like you have struck the Uppercase/lowercase bug in Lightroom.