Just to confirm the full process I have just gone through it on a machine.
1: First place a clean SxS card in the EX-1 and from the media menu format the media.
2: Connect the camera via USB to the machine, I have an XP machine, and delete the two XML files in the BPAV dir.
3: Copy the MP4 files into the sub dir CLPR, from your machine.
4: disconnect the USB and you will get a message on the EX-1 that asks if you want to restore the media? You do this and the EX-1 shows the video clips in the clips windows etc.
5: Connect the EX-1 camera backup to the machine with the Sony XDCAM EX ClipBrowser V2.0 and view the video clips on the USB disk. At this point the ClipBrowser will move the clips and re-build the BIM, PPN etc files in the original directory on the SxS card.
Hope this helps.