You might want to check this post: https://forums.creativecow.net/thread/142/875625 and this may be a more pertinent post: https://forums.creativecow.net/thread/142/867375#867382
I had this happen to me once after I instructed a cameraman on how to ingest XDCam footage by using XDCam Browser. Instead he moved only the mpg4 files over. It really screwed things up for me. Calibrated software was the only solution. I take it you have the XDCam drivers in place?
So a thought is to create an empty, new BPAV folder and copy the Mpg4 files into the same CLPPR folder in the right place and see if you can use XDCam Transfer to get them over into FCP. Make copies of the Mpg4 files though, just in case.
So XDCam is made to work through BPAV folders and the entire BPAV folder must be moved properly, and I use XDCam Browser for that, into its own exclusive folder, taking care not to overwrite the BPAV folder that might be there from another card.
This same kind of problem raises its ugly head on these posts quite often, cameramen not familiar with how to ingest and save footage properly. Your footage is still there, but Calibrated may be the only solution for you. You can download it for free but it has a watermark until you purchase it. Good to test it first.
Greg Ondera
http://www.Plexus.tv
http://www.SurgeonToday.org