I dont know if this will help....
I had a Primary Child Site that I had to remove and reinstall into a Secondary Site on the Same server. The CD that was given to me was an Eval (so guess what?) I had to uninstall the Secondary and wipe the server and reinstall as a Secondary with the same site code and hostname. Confused yet? Anyway I followed the uninstall directions from MSPress (SMS 2003 Companion) Chapter 2 and Chapter 4.
Remove the Site with the CD that you used to install it. Remove SMS Files and Folders from the Server. Remove Reg Entries. Remove Accounts from Local Groups. Wait for Replication.
This seemed to work for me and my secondary site is backup and working. Have not had any issues as of yet. By the way the Secondary Site that I reinstalled added the local boundaries during install.
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Thanks and good luck.