[Tarana]

Fastest way is to use Calibre and create a separate library of what you want on both readers. Takes 10 minutes or less. Create library. Connect your Nook. Go to the main library. Sort ON DEVICE column which groups what is already on the Nook. Transfer a copy of everything checked to the new library. Now disconnect Nook. Connect Kindle. Upload it all. You only have to keep this 'reader' library up-to-date. As you read stuff, delete it directly on your device OR do the reverse. Delete the items you have read in the new library. Connect your device and open that new library. Select the device. SORT. Delete everything that isn't checked.

I do this periodically as I take a different ereader when I go care for a relative than what I use at home. I MUST use something with a light in it since he has very poor lighting.

Keep in mind that while this will work for 1000 plus books, the indexing will take much longer and drain your unit faster than you would normally expect. This is especially true if it hangs up part way on a single book.