Certain masters missing - unable to export photos

Note: I checked my Photos Preferences and 'Copy Items to the Photos Library' IS checked under 'Importing'

But has this option been checked in iPhoto, when you originally imported the photos? Photos, that have not been copied to the iPhoto Library on import, will remain referenced in Photos.

Do the photos that cannot be exported in a smart album (File > New Smart album) with the rule "Photo is referenced"? If the photos do not show in this album, they have not been imported as referenced images, but accidentally deleted from your Photos Library or the library has a corruption. In that case try first to repair the Photos library.

To repair the Photos Library:

• Make a backup copy of the iPhoto Library.
• Hold down the key combination alt/options key and command key ⌥⌘ while double clicking the Photos icon. Click the "Repair" button and repair the library. This may take a while for a large library.

Or have you ever been running cleaning applications like CleanMyMac2 to remove duplicates? CleanMyMac2 will replace the original image files by the edited versions, and when I tested it some time ago it deleted too many original image files, if a photo had several edited versions. Check, if the photos in question are edited versions of photos with more than one version. In that case you can try to recreate the version with the missing original by duplicating the first version again.

I have searched for the filenames of the photos causing the problems in Spotlight and Finder, and I have gone into the 'Masters' folder in iPhoto Library to search manually, and the masters for those photos appear to be missing. Basically my question is: What do I do from here? Am I going to have to simply delete these pictures from Photos, find an old backup (which will be a nuisance) and reimport them?

Restoring from a backup will be the only way to restore the originals, if these particular photos are important to you. Or you could try to find the previews or thumbnails of these versions in the library, if you cannot find the original master files. But they will not have the full resolution.

and I have gone into the 'Masters' folder in iPhoto Library to search manually, and the masters for those photos appear to be missing.

Where in the Masters folder have you looked? The Masters folder is organised by the date of the Import Session (Year, month, day), not by the capture date. If your Photos library is a migrated iPhoto Library and you still have the iPhoto Library, open iPhoto and, select one of the missing photos and use the command "File > Reveal in Finder > Original File". If iPhoto also cannot reveal the original, try to reveal another original, that you imported at the same time, but where the original is not missing. It should be in the same folder as the missing original.

If the original master files are still inside the iPhoto Library package, the free trial version of iPhoto Library Manager could be able to repair the connections.

Download here: http://www.fatcatsoftware.com/iplm/

Here is a Help page:

Rebuilding a corrupted iPhoto library

You're welcome.