Photos says its a duplicate on import but cannot find it

I have *way* more problems with importing photos than I imaged. I have about 13.000 of them on a NAS in an elaborate folder structure, and all kind of weird things happened. Like in some folders only a few of the photos seem to have been imported. It seems that the import cannot be trusted, so now I've copied all my photos from the NAS (SMB) to my MacBook Pro desktop first, and am checking folder by folder.

When a number of photos are missing from a folder, I think the best strategy is I think cmd-delete them all in the album in Photos, and import them again by drag-drop from finder to that folder. Then I can see if I have them all, and they are in the right folder/album.

Latest crazy thing: On a drag-drop, Photos is telling me: "Would you like to import the following duplicate item?" Uhm no, so I cancel and use search to find the photo (by filename): no results. So the import bit seems to think the photo is already there, the rest of Photos does not.

Already repaired the library, tried all kinds of other ways to look for it (also via the PowerPhotos app/plugin): nope, does not show up.

Anyone an idea?