#1. "RE: My 2 Vaults disappeared?" In response to Reply # 0
Sounds like it could be a Permissions (OS issue) problem. Things don't usually disappear if not deleted. You most likely get an error of not having permission to access drive X. You redid the Vaults now - but I would still run Disk Utility and repair Permissions for your computer. And use Disk Utility to Verify the Hard drives storing your Vaults.
To do this the absolute best way, boot up from your install disk another disk with a OS backup of the OS, or Boot into the Recovery Partition of the OS, and run Disk Utility from there.
For me, repairing Permissions has solved for PITA issues with Aperture than anything.