Offer to re-import and re-link files which are missing but in database.
A somewhat tricky situation
The other night I was importing a lot of images and was distracted / impaired by beer. I know it's the users fault, one should not handle database modifications when not 100% alert. Anyway, there were some folders with ~6000 baby pictures which were copied manually in the watched directory. I was trying to make shotwell sort them in the YYYY/MM/DD folder structure, so I moved the images out of the folder, then dragged them into shotwell. A message popped up telling me that they are duplicates. I concluded the images where already there and thus the folders may be deleted. However, what Shotwell was trying to tell me was that the images are referenced in the database (but actually missing) Thanks to photorec I was able to recover the images.
Possible solution
It would be super live saving (for careless or intoxicated users) If shotwell would ask instead: "The images you are trying to import are referenced in the database but missing, should I import them again and re-connect the references?" Or something along the lines.