I was having some issues integrating Windows Server 2003 Service Pack 2 into a copy of Windows Server 2003 Enterprise R2 x64. The updater would keep reporting this error and bomb out:

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Service Pack 2 Setup  
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Failed to copy some or all of the files necessary for integrated install.

Please check that:  
a) No network or copy errors occurred during the integration process  
b) The format of the destination directory is correct.  
The files to be integrated must reside in an i386 and/or ia64 or nec98 directory  
(i.e. for an i386 share, if you typed "update /s:c:\cdshare", the files must be in the c:\cdshare\i386 directory).  
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OK  
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This stumped me for a bit, even after recopying the installation files from the CDs again and getting the same error. I then tried starting from stratch again and deleted the source files using the RD command. This command failed on a couple of files and to delete them I had to remove the Read Only attribute. So after recopying the source files and then removing the Read Only attribute for all the files, the Service Pack integration worked. It’s funny sometimes how the simple things can trip you up.