I've had a referenced library of photos in Aperture for years, but after moving to Photos (2.0 on Sierra), I wanted to consolidate them so they could be on iCloud Photo Library along with the photos I take on my iPhone, etc. The referenced photos are stored on my home network file server (just a little box running FreeNAS that I use for Time Machine and my photos). I already have about 34,000 photos in iCloud Photo Library, so I created a new account on my Mac, took my newly converted Aperture library and opened it in Photos and then enabled iCloud Photo Library.
Naturally, the 110k photos that are referenced weren't added to iCloud, so I clicked the consolidate menu option. That began a week long (ongoing process) that goes like this: every 5-30 minutes, Photos pops up asking for permission to access one of the folders in the referenced library (which has Year/Month/Day subfolders). I click approve. Occasionally, it finds an image it can't locate, I show it where it is and most of the time it returns an error. The rest of the time, it keeps moving along, but at a snail's pace: after a week, it has consolidated about 4,000 of the 110,000 photos. This is not a problem with the NAS, which is fully capable of keeping up with a gigabit ethernet connection.
The little progress circle is stuck in the same position. When I click on it, it says "Reconnecting Referenced Media" and the progress bar has literally remained unmoved for days at about 1/3 of the way. Photos crashed, I restarted it and it resumed at that same point.
This leads me to a general and a specific question: generally, is there something I'm doing incorrectly that would lead Photos to running at an almost hopelessly slow speed consolidating this library? Specifically, is there a way to grant blanket permission to Photos to access the referenced photos' folders so it doesn't keep stopping to ask permission for seemingly every single folder?