Photos missing in iCloud Photo Library

I have successfully imported my Aperture Library into the new Photos app on my iMac - 17866 photos and 485 videos.  All seems fine.
I then turned on the iCloud Photo Library and left it to upload overnight.  18 hours later it says 'Updated Just Now', and seems to have stopped uploading.  However, when I access the library on iCloud.com, it contains 4794 photos and videos only.  I think all the album structure is there, but many of them are empty.
My Aperture library was a referenced library, with the originals stored in the Pictures folder (not in the Aperture library).  I have read today that referenced libraries will not upload to the iCloud Photo Library.  My library also contains many Photostream imports from other devices - I don't know if these are referenced.
Can anyone help me with these questions:
1. If referenced photos will not upload, why have some of mine been uploaded and not others?
2.  How can I pull these referenced photos into the Photos Library (ie. un-reference them) so that they will upload onto the iCloud Library - if indeed this is the reason they are not uploading.
Hope this makes sense to someone out there.
Many thanks in advance.
Judith

I think I have found the solution on another thread.  Am consolidating the referenced files which will hopefully solve the problem. A bit puzzling that I didn't get the warning some people mention, that the referenced files would not be uploaded to iCloud.

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