Turn on iCloud Photo Library without creating duplicates or zombies
In theory, it will detect all the duplicates on your Mac and not upload them. I suspect, but don’t actually know, that a photo on your Mac that you’ve previously deleted from iCloud Photo Library by deleting from your iPhone is going to get uploaded again. One thing you might want to do is create some albums on your iPhone and your Mac that you can use to look at what happened. For example, if one album has all your Mac photos in it while another has all your iPhone photos in it, after the upload completes, you can create an intelligent album of all the photos that were on the Mac but not on the iPhone during the time period that you took your iPhone photos. Those are likely to be the ones you deleted. Photos in Recently Deleted might get picked up as already deleted. Or maybe the engineers were super clever and have a checksum log of every deletion ever made. 

Also, when you enable iPL on the Mac, iCloud is going to want you to have sufficienct space available to add every photo on the Mac (since it doesn’t know about dups yet) so you may need to increase the amount of space you are buying. You can reduce your plan after it’s completed if you don’t actually need the space.

The reconciliation can be a long process (days or even weeks) depending on the size of your library, the speed of your Mac, and the speed of your connection. It doesn’t actually upload duplicates, it just does some kind of a checksum comparison to detect them.