Ok, I have an HMC40 (uses the same folder structure)
First - DO NOT pull the stream files (or any other for that matter) out of the AVCHD folder structure. If you want to backup the card, copy the PRIVATE folder to where you need it.
Second - DO NOT attempt to import the stream files directly into FC - AVCHD spec is not edit friendly. If you are importing from PRIVATE folders that you've copied (for example, you may have a folder on an external drive called Archived Footage, then in there you'd have folders for each card you archived, like let's say May 13 - 2010 - Card 1, and in that folder would be the PRIVATE folder. Then in FCP if you need the footage, you use log and transfer, click the plus sign on the folder in the upper left corner of the L&T window and navigate to the May 13 - 2010 - Card 1 folder and let FCP parse the folder and offer the footage for importing into your project. At that point, FCP will transcode to ProRES for editing.
As long as you leave your footage in the AVCHD structure that is on the card (at least don't change/rename/modify the PRIVATE folder) FCP should be able to work with it without issues. You can test this by copying a card over to a hard drive then using the import instructions from "Second" above.
Hope that helps.
ps - that is how I archive my footage, I put the AVCHD folders only an external drive for long term storage.