Covers and management

[s36x]

2 Questions here:

1) Every single book in my Calibre library has a cover in it (I checked the metadata to make sure.) But my Nook Tablet doesn't recognize about a third of them (they were stored in my Nook's memory now they're on an SD card. Same result) I looked at the files (the opf file) and they all have a "Cover.jpg" file listed. I noticed though that in the folder on my SD card where the covers were stored (.docThumbs) all my covers were there except the ones that the Nook doesn't see.

Is there anyway to extract the cover from the calibre metadata and copy it to that folder? And then will the Nook will recognize it?

2) I know that if I edit metadata on calibre, it won't "overwrite" the book's metadata on the Nook (I already asked that one) but now that my books are on the SD card, have I overcome that issue?

Thanks for the help!