iCloud Photo Library activation on my phone deleted majority of pictures
I'm adding a summary of the discussions the OP and I had when trying to troubleshoot this issue.

This issue was due to how the OP copied the original photos: iPhone -> Mac -> iCloud.  The photos remained on the iPhone and the assumption was that iCloud would not have to do much work at all.  The exact same photos that were uploaded and sitting in iCloud were sitting on the iPhone. 

The photos first had to be synced to iCloud from the Mac. With the large number of photos involved, that took several hours to complete. 

After that, iCloud then begins to sync the photos back down to the other devices signed-in with that same Apple ID, in this case it was the same iPhone.

The iPhone will only perform iCloud photo syncs when the device is on wifi and plugged-in to power (with iOS 11, you have the option to allow syncing on cellular connection via Settings -&gt; Photos -&gt; Cellular Data and turning on Cellular Data).

iCloud took over 9 hours to sync the photos back down to the iPhone, replacing all the exact same photos that were already stored there.

To avoid this, sync the photos from the iPhone -> iCloud first.  After that, it will sync down to the other devices, like the Mac.  It will still take several hours depending on how many photos are being synced.