If I transfer files to a new hard drive and "special permissions files" are

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I am installing a new, larger, hard drive in my Powerbook G4. I want to "clone" the old hard drive onto the new one. However, when transferring files to a PowerMacG4, as an intermediary in the process , via Target Disk Mode , I get the message that "certain files with special permissions will not be copied".
I did check the messages in this forum and found that there is a way around this problem. However, it seems that I would need a clean hard drive to do this and I don't want to reformat my G4 PowerMac in order to use that drive as an intermediary in the process.
The simple question is then: What will happen if I copy the G4Powerbook files via Firewire to the G4PowerMac drive, ignore the permissions warning, and then transfer that data to the newly installed drive in the Powerbook???? Will there be important systems files missing, or will some of my programs simply not work. Perhaps I could then just reinstall anything that's not working (that required special permissions)?
This probably sounds like a stupid question to you Mac gurus, but I've never really understood the significance of "permissions".
You cannot simply copy files from one drive to the other. Also, if you clone to the hard drive in another computer, then you must use a separate partition on that drive. You cannot clone to a drive that already has OS X installed on it.
The cloning process works as follows:
How to Clone Using Restore Option of Disk Utility
1. Open Disk Utility from the Utilities folder of the drive you are cloning.
2. Select the backup or destination volume from the left side list.
3. Click on the Erase tab in the DU main window. Set the format type to Mac OS Extended (journaled, if available) and click on the Erase button. This step can be skipped if the destination has already been freshly erased.
4. Click on the Restore tab in the DU main window.
5. Select the backup or destination volume from the left side list and drag it to the Destination entry field.
6. Select the startup or source volume from the left side list and drag it to the Source entry field.
7. Double-check you got it right, then click on the Restore button.
8. Select the destination drive on the Desktop and press COMMAND-I to open the Get Info window. At the bottom in the Ownership and Permissions section be sure the box labeled "Ignore Permissions on this Volume" is unchecked. Verify the settings for Ownership and Permissions as follows: Owner=system with read/write; Group=admin with read/write; Other with read-only. If they are not correct then reset them.
For added precaution you can boot into safe mode before doing the clone.
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