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Farsider

macrumors 6502a
Jul 30, 2014
629
306
London, UK
Yep, I had the same problem after an iTunes restore on an iPhone and a TimeMachine restore on a Mac. iCloud Photo library appears to take all these photos as new photos and started to upload them all. I didn't wait for it to finish so it could've magically fixed itself but I didn't want to find out.

I nuked my local Photos Library on my Mac and all photos on my iPhone and let it re-sync from scratch.

That's clearly not how it should work but all is OK now.
 

Farsider

macrumors 6502a
Jul 30, 2014
629
306
London, UK
If iCPL is off on your phone and Mac. Deleting photos is quite safe.

You can always restore from your backups should the worst happen.
 
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