It is unlikely that the .iso was damaged, because the ramdisk kernel will compare SHA checksums against the base46.tgz file. If you still have the .iso handy, you can inspect the contents of the base46.tgz fileset yourself.
It is unlikely that hard drive bad sectors are the cause, either, as you would get I/O error messages on sector reads, not missing files.
The most likely cause is a finger fumble of some kind while you were logged in as root. Best practice for admins is to use sudo(8) or su(1) and a normal user, to prevent mistakes of this kind.
If you do not have a recent backup which is undamaged, you -must- reinstall, as merely recreating the library file will not ensure a complete and undamaged system.
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