Managing videos on my new camcorder

Last week I bought a new Sony HDR-CX7 high-definition camcorder. It records to Memory Stick flash-drive and includes a docking station that both charges it and allows direct download via USB cable.The videos are stored to the memory card in the folder, /avchd/bdmv/stream/ *.mts
The problem is figuring-out how to move the files onto the computer without the camera freaking.

If I simply copy, then delete the files, they will still appear in the playlist and give an error if you try to play them. If I delete all the other data files under /avchd then the camera asks you to re-initialize the memory card. I've yet to find a way to remove the .mts files without requiring extra steps on the camera afterwards.

By comparison, with my Nikon digital camera I simply copy the .jpg files and then delete them. The camera recovers from the unexpected disappearance of the files without complaint.

P.S. Kudos to Sony on their docking station's USB interface -- the memory card is easily recognized by Ubuntu Linux. This is in stark contrast to my LG 'Muziq' phone, which has a USB interface but tries to present as both a memory card and a modem, interfering with Linux recognizing the card. It's a cool idea, to be able to use the phone as a modem, but it's only supported in Windows, blech!