I have some corrupted files on my OS9.2. hard drive that won't delete.

My computer is in three sections, the OS X is fine, but both OS9.2 drives are causing me trouble. The additonal OS9.2 drive is purely for music, but originally my audiophile card 2496 was installed on both drives. I had a problem with the sound on the small drive so I uninstalled everything and then reinstalled it all. The music records alright now, but when I close Cubasis it freezes on the small drive . When uninstalling all the music I found I couldn't delete all the audiophile card files that were on the main hard drive - they were in an invisible file marked usr (that is the spelling used) and the rest of the path was greyed out. I tried to delete them straight from Sherlock but to no avail. I am wondering now whether to reinstall the OS9.2 system on both hard drives but need to ask a few basic questions. When I do this will this fix the 'corrupted files' that are already there or will this cause more trouble. Will I lose all the work that I have already done on these files or should I make sure and do a back-up onto DVD just in case. How does one reinstall the Operating System? I have the disc but just not sure what to do as I haven't done it before. Will these corrupted files do more damage to the computer if I just leave well alone - it is a nuisance restarting the computer every time I use Cubasis but I would sooner do that than get into more of a muddle than I am in at the present.

Hi, peckerpac -
If I deep-wipe the drive what exactly does that mean?
That means the drive is effectively stripped of all data, including the removal of the disk directories. A file (or folder) that refuses to be trashable indicates there is probably damage to the directory. DiskWarrior usually can fix that; apparently not in this case.
Once the drive has been stripped, the initialization process creates a new structure on the drive so that it is usable for data storage, including new directories.
When you say I can't deep-wipe a partition, do you mean that the whole Hard Drive OSX as well will be deep wiped, or does it mean that only the OS9 part that needs it will be wiped?
A hard drive that has been partitioned has had its disk subdivided into two or more volumes. For most things the Mac will treat each volume as if it were a separate hard drive - each volume will have its own icon on the desktop; files can be copied from one volume to another; if each has an OS, each will appear individually in Startup disk control panel and in Startup Manager; etc.
However, although the Mac treats each partition as if it were a separate drive, they aren't - they are still part of the same physical drive.
A single partiton can be erased, for example by using the Erase function in the Special menu in OS 9. Unfortunately all that an Erase does is to delete entries in the disk directory - none of the data is actually removed, including the directories themselves.
A deep-wipe of the drive is part of a broader initialization of the drive; this affects the entire drive, meaning all partitions of the drive will be wiped of all data.
Will I lose everything when I deep wipe the drive?
Everything that is on that drive, on all partitions of that particular drive, yes.
As Grant noted, the Big System Morsels error usually indicates a problem with the machine being able to read the CD properly. Often that can be fixed by cleaning the CD. A Mac's optical drive is far less tolerant of smudges (fingerprints, etc.) on a data disk (such as an install CD) than it is with such on an audio disk.

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