Background: I am working with FCP7 on 10.6.8. As far as hard drives go, this problem has hit me on USB 2 & 3 and firewire800 drives.
Either way, I'm working with footage that I shot on an FS700 (to the SD card) and I'm having huge problems.
I bring in the ProRes footage with Log and Transfer on FCP7 and all works fine. I start editing without problems, but then something weird happens.
Sometimes when I open FCP again, it says random files are missing. I check the Capture Scratch and they are in fact, not missing. They are right there. I reconnect the files, but then instead of bringing the right files, it brings in random ones.
Say, clip 100-120 are offline, when I reconnect the files it brings in clip39-59. So the file says clip100, but it'll be the same thing as clip39.
Then, when I go back into the Capture Scratch, the files have literally been re-written so that clip100 is literally the same as clip39.
Sounds like a job for Disk Warrior. It rebuilds your disk's directory. I use it once a month to prevent weirdness and always when weirdness strikes. IMHO, it's the one program every Mac user should have. It's saved me many times.
MacPro 8-core 2.8GHz, 16 GB RAM, OS 10.9.4, QT10.1, Kona 3, Dual Cinema 23, ATI Radeon HD 5870, 24" TV-Logic Monitor, ATTO ExpressSAS R380 RAID Adapter, PDE enclosure with 8-drive 6TB RAID 5
FCP-X 10.1.3, Motion 5.0.7, Compressor 4.0.7
FCS 3 (FCP 7.0.3, Motion 4.0.3, Comp 3.5.3, DVDSP 4.2.2, Color 1.5.3)
Pro Tools HD 10 w SYNC IO & 192 Digital I/O, Yamaha DM1000, Millennia Media HV-3C, Neumann U87, Schoeps Mk41 mics, Genelec DSP Monitors, Prima CDQ120 ISDN