Ahh, you are actually deleting the calibre book record then re-adding it? Why? It seems that you should replace the format in the book record, not re-create the record. It is trivial to replace the format; simply show the book details for the book in question then drag the new book file onto the cover image.
In any event, the problem is that the file name template you are using for sending books to CC does not use the book ID, so CC thinks that the two books are the same calibre record when in fact they are not. This is the same situation that arises if you have different books with identical title and author in which case the last book sent wins. To avoid this difficulty you should add the book id to the template (see note #3 of
this FAQ). Once you do this then any replaced books will no longer show as on-device and won't sync metadata.
As for not knowing if books are up to date, you can solve that problem by resending all the books to your device. Connect, search for OnDevice:true, select them all, and send them.