I found a problem when I tried to re-run an import when I am renaming my image files and I also have "Make A Second Copy" enabled.
I was making and testing a new import preset in a test catalog and I made a mistake in the destination. So I removed all the images from the catalog, deleted them from the disk and removed the now empty folders.
After I corrected my import preset I reran the import with the source as the same input card. This time the import proceeded almost to the end but then displayed an error dialog saying LR could not rename any of the images it just added to the catalog. I click continue and go to the Previous Import in Grid view
Everything is pretty messed up at this point. All the thumbnails in the Grid have the original name from the camera. (IMG_2449.CR2) and the missing file question mark badge. The image files in the Library folder are the correctly renamed files (sherwin_20121015.cr2) and the backup copy folder (Imported on November 9, 2012) has one of each.
It gets even more confused because when I tried to clean up by removing all the images from the catalog again that failed because and LR left all the renamed files in the catalog folder. Since I did not catch this on the first go the subsequent try created new image files all with a "-2" suffix because all the files were still there from the second import.
It seems like a simple fix would be to have every import get it's own backup folder. In other words don't just make one backup folder for each day. Some options for naming the backup folder would be nice too.