I'm running lightroom 5.5 on my iMac (OSX 10.9.3) and I recently had an issue where after opening LR, it could not find the RAW files. I found this strange because I never moved them. I looked through the trash bin and nothing. Searched through every hard drive and I couldn't find them anywhere. They hadn't been moved or deleted except they had gone missing completely. I thought it was just a one time thing and moved on with my life.
Today, my girlfriend went to export some photos from a recent shoot we did and found the same thing happened to her. Luckily we have the RAW backed up, but why is this happening. We didn't attempt to convert to DNG. She tried to export the jpgs and found that the folder containing the RAW had been "modified" three days ago. Yet, the files were not moved to anywhere else, were not in the trash bin (there were still files from two months ago) and had not been touched by either of us. The original containing folder had once had files in it because it still contained about 40kb of data but with 0 items. PLEASE HELP!!! We are wedding photographers and this could potentially lose us thousands and thousands of dollars and new potential clients!!!
Nothing you have said indicates Lightroom was the cause of these problems.
When you did the search, did you look with your eyeballs, or did you use the search feature on your MAC to search all hard disk(s) for at least one of these files by file name?
Restore the photos from your backups. Just copy (not move) the backup files to the folders where Lightroom expects the photos to be.
I always look with both. I exhaust my eyes and then use the search bar for all hard drives. I can restore the photos and LR still has the catalog so that's not an issue. I also run a program called Onyx to clear out my memory cache. I wonder if that program may have something to do with it.