[I haven't read above reply yet but thankyou for it...In the meantime...]
I suspect part of the problem is that the books have different names as raw epub/pdf files, versus what they are named in Calibre
(Admittedly I did also add a heap of books that are NOT in Calibre)
This video partially answered my question:
Calibre: Adding Books from Library to Device or Device to Library
Here is my plan:
1. Keep all the books on the Kobo nicely organised into various folders (as I said, for Koreader and Plato)
2. Use the method described in the video to put the books that are NOT being detected by Calibre, INTO calibre.
3. Now I will have some duplicate entries in the library.
But MANY will be the BETTER entries that have all my nice shelf info.
So I do the following...
4. FIND DUPLICATES using the plugin with that name
5. Go through the duplicates and use EDIT METADATA > MERGE BOOK RECORDS
to delete the books that have the useless metadata, leaving only the books with the good metadata
6. I expect it wont find all of the dupes, because some will have slightly different names or sizes.
So I will order by name then by size etc in Calibre to repeat step 5
This is my rough plan!