[parking]

I am trying to use a sony prs-t1 with calibre. I have downloaded the prs-t1 plugin, and set epub as the first format, followed by pdf and txt.
I have 500 plus books in My Callibre Library, all set up under a folder with author's name, under this a folder with individual book name followed by a number in brackets, under this a folder with the epub file, the metadata file and a cover.jpg file. I presume this is the normal Calibre setup method.
When I selected Send to Device 200+ of the books went to the device without a problem. The remainder lost the picture of the cover in Calibre and would not transfer because "no suitable formats were found". When I answered yes to convert to suitable format, nothing happened.
Then I went to find a cover jpg for one book, so selected "edit metadata individually", and browsed to the folder where the cover is stored. selected it and said OK. A window popped up and said "OS Error No such file or directory". I said OK. A second folder has now appeared with the book name and a different number in brackets. Opening this folder there is only a metadata file there. The book cover does not update in the calibre display.
If I go through the process again the book cover does appear and saves ok, But I am now left with 2 folders for this book under the author's name.

Can somebody please tell me what I am doing wrong here, why some books transferred to device ok, and some didn't, and those that didn't lost their cover data even though it was still there.

Sorry to be so long winded with the question, but I want to use Calibre, but I also want to understand what is happening.