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I have seen this problem too. Above the folders section in Library view theer is a missing files folder, click on it and it shows files. No question mark on the files and if you click on show in finder it shows it in its correct location. If you click on remove it will remove the file from disk and not the database.
I think mine went away when I moved the images offline and relinked them.
Is this the "Missing Files" temporary collection in the same pane as "All Photographs"? If so, it means that the database has lost some of the location information for them, not that they are physically missing from the disk. I believe it's a catchall for situations that Lightroom can't handle. I don't know if 1.3.1 handles this temporary collection better than 1.2 (per your sig) as I've not had the problem since 1.2.
The way I got around it was to locate the photo folders within Lightroom and export each of these folders as a new catalog. I can't remember whether I included negatives and previews but I think I did. The first time I tried I just exported the missing files from those folders but as some of them were in stacks the new catalog didn't know about the stacks so it is important to export the whole folder.
Once I'd checked that the newly created catalogs had the correct photos, I removed (not deleted) the photos from the "Missing Files" collection which also removed that temporary collection. Importing from the new catalogs put everything back how I expected it to be.
I had this problem after loading 1.3 and 3'% of my files read " Files missing or offline" these files were random, as some were missing even on the same shoot. As I had only just started using Lightroom, deleted all the files and re loaded from my external hard drive. Everything is working fine now, but would also like to know why this happens.
