I have this same problem. About 400mb of data and it takes FOREVER to do this. I'm not sure how long exactly, but upwards of 3-4 minutes.
I generally hit 'O' on whatever I'm looking for and close Calibre before I plug in my DX and then just move the file manually.
I'd really prefer it not do this or some ability to turn off the feature myself. I never move files the other direction.