Thanks for raising this. I do not have a solution, but am another person with the same problem. In fact I am getting rather alarmed that Apple is going in the direction of Microsoft with sending out incomplete and buggy updates. I am wondering of this will be a trend and I need to go back to my PC days... What with iMovie crashing since the Sierra update, playlists not syncing between my Mac and iPhone and iPad, the iPhone freezing again and again in the Phone app, and now this major issue with Photos...
Ok, so let me get to the issue. I upgraded to Sierra Nov 10, and it took forever for my old Mac to scan all the photos (there should be an option to turn off the recognition feature, I do not really care to scan for 'cows', and I need my <ac to work as opposed to being stuck in limbo for THREE days). Yesterday I opened Photos, as have been travelling extensively in Asia past few weeks, only to discover that all my folders, literally hundreds of them, that I have had from the iPhoto days, have been deleted (or at least do not appear in the sidebar on the left). I looked up any help online, there were some threads, then repaired the library. I did get some of the Smart Folders back, but only those and not the regular ones, and it looks like the contents of some of them are not complete. But today, as I contemplated restoring my TimeCapsule backup of Photos from Nov 9, I noticed that all photos from about end of Jul to Mid Nov are gone... All my holiday photos from France and Switzerland!
OK, so is there anything I can do about this? Find the missing photos? The missing folders? Or is my only option the route of restoring the old library from Time Capsule prior to the Sierra update, exporting the photos since Nov 10 from the new libabry to the old, and them making the old the default? Or will the same thing happen with the recognition scanning?
Or should I just go back to a PC and an Android phone and stop wasting my time on fixing Apple bugs that seem to become more and more prevalent...