IPhone – App has photo access, but I never allowed it to access photos

See https://apple.stackexchange.com/a/180313/54484

The files were not duplicated, rather additional hard links were created. The data exists once, and each hard link is simply a pointer to that data on the hard drive.

Deleting one library will not recover any significant space, because hard links to the same data still exist. Finder shows the size for each library bundle as including the hard linked files, so it appears that much more space is being used, when it is in fact not.

As far as your "missing" 33 GB, unless you have turned on the display of hidden folders you are not getting an accurate count by simply counting the size of visible folders. Use something like Daisy Disk for a true view of what space is being taken up and where.

Finally, for the record, both Aperture and iPhoto work fine under Yosemite, so long as you don't delete the libraries they used. They cannot read a Photos format library.

You could try backing up the iPhone in iTunes and dig into the backup locally to see if the photo files are in the app's backed up data. I work on a tool that can help you dig into the backup files, Decipher Backup Browser: https://deciphertools.com/decipher-backup-browser.html

You could either look through the app's data in all files view, or try the all photos gallery view in DBB. Or if you want to contact me directly about searching around the backup, there's a contact link at the top of all of our pages.