Re-Install SMS Secondary Site

What I would recommend:
1) Run PREINST /DELSITE on all
primary sites in a direct line up from this site
2) Uninstall the SCCM Secondary site again
3) Remove all entries from AD about this site
4) Run the following query that should return 0 rows in the database
Select * from Sites where sitecode = '
site>'
5) Look in SCCM\Inboxes\ReplMgr.box\History on the parent site for a file by
the name of .TRS and delete it if it exists
6) Reinstall the secondary site

When all else fails:
Copy the site control file from the secondary site to a local folder
and rename it to SITECRTL.CT2. Place the renamed file in the HMAN.BOX of
the parent site and monitor the HMAN.LOG for entries pertaining to the new
secondary site. Refresh the console and you should see the new site. Keep
in mind that this procedure does not correct any communications issues.