If the firewire comes out, it stops recording of course. You just need to reinsert it and start recording again. This can corrupt a clip, but just use the “repair clip” option in the FS-100 and it will be good until the cable was pulled ;>).
As far as the Quicktime clips, they are all broken down into individual clips due to the FAT 32 limitation of the FS-100 Hard Drive.