Photos app not uploading all photos
Options 3,4 was the only ones that worked for me, but no guarantees...


Holding Opt+Cmd while opening Photos, to do a "Repair".
Selecting to keep originals on the computer, not optimize" them.
Carefully wipe what you have and start again.  This should include deleting "Events" folders in iCloud.com>Photos, before swapping libraries on the computer, to avoid orphaning them. See below...
Use "iPhoto Library Manager" to "Rebuild" the original iPhoto Library, then re-migrate.  This assumes you have backup of an "un-migrated" version, in Time Machine or elsewhere.  I had a folder with 1.6Gb of iPod thumbs in my original library.  Also, I think it may update the Last Modified" date to help the upload.  I'm not sure why it worked..


How do I delete Unlinked folders

iPhoto Library Manager