MacOS – iPhoto “A photo Has been found in the iPhoto library that was not imported”

If there aren't many photos, the easiest way to do it is simply delete the photos on the phone. Unfortunately, this means selecting each photo individually as there is no 'select all' option.

To avoid individually selecting photos on the iPhone, you'll want to use the 'delete' option when prompted at the end of importing. Because iPhoto only deletes the photos that were imported at that time, you won't be able to do this with your 'normal' iPhoto library. To get around this, simply create another (throw away) iPhoto library to import the photos. Select 'delete' when prompted at the end of the import to delete the photos from the iPhone. Then you can delete this throw away library on your Mac.

To create a new iPhoto library, hold down the Option ⌥ key when launching iPhoto. This will display a window asking which library you would like to open or create a new library.

It is a bad idea to try to manually modify the folder structure inside the iPhoto library, as you seem to want to do.

The best way is to follow Apple's instructions for rebuilding the iPhoto library.

However, this is usually only used as a repair procedure if iPhoto is malfunctioning.

You can try this, but make sure you have a complete backup of your iPhoto library before you start the rebuilding procedure.

Also, realize that iPhoto has an internal Trash that is separate from Mac OS X's Trash. If you have deleted hundreds of photos over the years, and never emptied the iPhoto Trash, those photos will still be in there and taking up space in the file structure.