PPSH2024 wrote: .. I used export to export on desktop (not as "unmodified")
and I drag and drop to re-import - does this affect the process ?
Have you done lots of editing? It seems to me you'd want to modify the original. Drag & Drop can't always be depended on, but it does seem to go through the normal import process, which checks for duplicates. So I think the process is OK.
The thing is, the import process checks against the database, and the database takes a bit to get updated. My guess is that you imported these files pretty quickly after doing the final delete, so the database didn't have time to update. Try again, but give it some time.
My biggest question is, why are you changing the file name. The filename pretty much is totally ignored in Photos, and you can give a new file name when you export pictures. The filename does appear, for reference, in the info window, but so does Caption and (on a Mac) the title. The title shows under the thumbnails, and you can sort by title. You can search through titles and captions which can carry more information. When you export a picture you can use the title for the filename.
You can also export a set of pictures with sequential filenames, like Grand Canyon #17 etc.

So the filename really doesn't matter much. But I understand you may have your reasons-- just hoping to save you trouble in the future...