It's simply as I said.
I add a book to Calibre and it's on the Kobo with all info/metadata.
I add another book from the Calibre library to my Kobo and as soon as thats added you can see & watch the green tick disappearing from another that you previously had on the library. I checked the Kobo after disconnecting it properly - the new book is there and the 'deticked' book has gone. I found some of the 'disappeared' in seperate folders in Kobo - although all info was there previously ( author, title etc) and now its showing up in these folders as title unknown/author unknown.
Many thanks for everyones help, but I have now given up with calibre and moved on EPUBOR Ultimate which although has no library as such, allows me to convert the books to EPub and they don't delete.