After cloning hard drive, aliased folders appear

Recently I cloned the hard drive on my PowerBook G4 (source) to a new external drive (destination) using Disk Utility.  The process went well.  However, on the new drive, 3 aliased folders appeared, "etc", "tmp", and "var".  I believe these are hidden folders from the source drive which I can see by using OnyX on the source drive. My question is, how can I re-hide the folders?  Can I delete them?  The new drive is now in my PowerBook and I don't want to reverse the whole process of swapping drives.  Should I startup from the external FW drive, reformat the PowerBook drive, and clone the external drive to the PowerBook drive using CarbonCopyCloner. Will this solve the problem or make it worse? Seems to me that there should be an easy way to hide the visible aliased folders.  After all, the developers did. I have tried the program "Hide Folders" but permission limitations prevented the process.  Will a reinstall (not clean) of OSX eliminate the aliased folders? Any thoughts would be greatly appreciated.

how can I re-hide the folders?
Hidden files will be visible on non-Boot drives, perfectly normal.
Can I delete them?
NO, NO, just leave them, they are needed... in fact the reason they are hidden on the Boot Volume is so you don't do that & render it unbootable.

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            Encryption Type:         AES-XTS
            Conversion Status:       Complete
            Conversion Direction:    -none-
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            Fully Secure:            Yes
            Passphrase Required:     Yes
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                Revertible:            Yes (unlock and decryption required)
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                Volume Name:           Macintosh HD
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    devfs on /dev (devfs, local, nobrowse)
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       Device Identifier:        disk2
       Device Node:              /dev/disk2
       Part of Whole:            disk2
       Device / Media Name:      WD My Book 111A Media
      File System:              None
       Content (IOContent):      GUID_partition_scheme
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       Media Type:               Generic
       Protocol:                 USB
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       Device Block Size:        512 Bytes
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       Read-Only Volume:         Not applicable (no file system)
       Ejectable:                Yes
      File System:              None
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       OS Can Be Installed:      No
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       Protocol:                 USB
       SMART Status:             Not Supported
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       Volume Free Space:        Not applicable (no file system)
       Device Block Size:        512 Bytes
       Read-Only Media:          No
       Read-Only Volume:         Not applicable (no file system)
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    belambert  ttys000                   Wed Mar 11 17:34 - 17:39  (00:05)
    belambert  ttys000                   Wed Mar 11 17:33 - 17:34  (00:00)
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    -bash: 2:: command not found
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    -bash: /dev/disk1: Permission denied
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    -bash: 7A998EAE-68FB-4BAC-BF40-7A31D2806B2C: command not found
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    -bash: syntax error near unexpected token `('
    ~ belambert$ |
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    -bash: Name:: command not found
    ~ belambert$
    -bash: 3:: command not found
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       Whole:                    Yes
       Internal:                 No
       OS 9 Drivers:             No
       Low Level Format:         Not supported
    :~ belambert$ Last login: Wed Mar 11 19:23:03 on ttys000
    ~ belambert$ diskutil list
       Whole:                    Yes
       Internal:                 No
       OS 9 Drivers:             No
       Low Level Format:         Not supported
    ~ belambert$ Last login: Wed Mar 11 19:23:03 on ttys000
    ~ belambert$ diskutil list
       Volume Name:              Not applicable (no file system)
       Mounted:                  Not applicable (no file system)

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    Re: Blinking Folder with Question Mark after Erasing Hard Drive to try to restore to Factory Settings 
    in response to Niel
    Thanks for the reply, held command+R again and it is trying to pick up WiFi, but it's not picking up my network and won't accept the password even when I try to put it in manually. Any thoughts on that?
    Me too had tried the command+R and failed to manually connect to my network. Can anyone help?

    Well, it was solved. I shifted to other place and tried other WIFis. One of the WiFi had the 2002f problem and another was fine, so the reinstall worked smoothly eventually.
    On the apple support page it says that Supported network configurations and protocols includs both WPA/WPA2, not matter what they are, but it might not be true.

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