Same question was posted a month ago by a different user, but she stopped responding... I have the exact same Issue.
This is a little complicated. I turned off iCloud Photo Library (for reasons that are unimportant) and the dialog that says "Photos will be removed from your phone, but will remain on iCloud" popped up and I hit "OK".
So 3100 photos were removed from my phone because they were all stored to iCloud.
Then I turned iCloud Photo Library back on, thinking all the 'removed' photos would reappear in my Photos App, but they didn't, and I don't know what to do. I verified that all of the photos are on iCloud by logging into the web interface on my desktop, I just can't get them to show back up in my Photos App on my phone.