In this instance I would use Sony's free Clip Browser to export the stuff off the card in its native format into a BPAV folder (as it will do in the process. At that point I would then use Sony's XDCAM transfer software to bring it from the BPAV folder into Final Cut. You can do your in and out points, if you wish or bring in the whole ball of wax into FC.
When you quit the XDCAM transfer software on the virtual card you are working on (BPAV folder) it will ask you if you want to save your work. If you do it will save your logging info which is, I believe, what you want to do.
Do a reformat of your SxS card with your EX3 once you are confident you have all the material from the card on your hardrive.
-Andrew