Photos Database Corruption
I wasn’t previously having a problem with Photos, but because I was having an issue with restoring to my new iPhone 7, so I repaired the database (after a Time Machine backup).
The Masters directory is still identical to its previous state, but many photos (basically, everything that was imported in October, and who knows what else) now appear to be missing from the Photos library. It was easy to see what was missing in a number of cases, because some are within albums and smart albums and have been synced to my iPad and older iPhone. Further, these files still exist within the Masters directory; they’re all still there. An attempt to add them back into the library, though, reveals the “duplicate photos” dialog box, and shows the appropriate thumbnail.
I do not have any hidden albums, and searches for the filenames within the Photos app do not reveal the missing photos that supposedly still exist within the library, so the files have disappeared into a tangle of broken database pointers, apparently.
Mac Pro, macOS Sierra (10.12.1)