"After 6 weeks of investigation, including 2 weeks of sleepless, active nights, we've nailed the problem. At its essence, the ATA-based Macs, most notably the 5xxx and 6xxx series, have been having troubles where the ATA hard drive gets horribly corrupted in some circumstances, leading to a flashing "?" on the screen at startup. Final effects usually include a near-total loss of all data on the drive.
The problem is a lineup of bugs in the ATA Manager, Apple ATA driver, and the drive firmwares. The problem is almost always caused by the ATA Manager disconnecting the drive from the System before the cache structures can write important directory data to the drive, or disconnecting it halfway through the writing.
Apple has just finished Drive Setup 1.3.1. It should be released to the public in the next few days, and will prevent the problem from happening. Anyone with an 040 or PowerPC based Mac using the Apple drivers should get this and use it to update their drive. You can check what driver version is currently being used by Getting Info on the hard drive's icon, and checking the parenthesis in the Where: section. Apple SCSI drivers will be in the 8.0.x range. Apple ATA drivers will be in the 3.0.x range. The new ATA driver is version 3.07.
One major item to watch out for is the Mac OS 8 Installer, which will change the driver back to 3.05. You will either need to update the driver after you finish the installation, or uncheck the Update Driver option in the installer before you install."