I used STSADM to export a site then imported it to the same collection but a different URL. I used includeusersecurity for both. The export and import worked.
But this destroyed security for some unrelated higher level sites. One Active Directory group completely disappeared from all of the broken sites and putting it back only helped in some cases.
Trying to fix some sites has not worked at all. Changes made to their security has absolutely no effect. I had to add users into a different already used Active Directory group to get them into the broken sites and this AD group is not even listed within
the broken sites security!
It's seems to be related to sites using Active Directory groups only. My sites with purely SharePoint groups seem fine.
I even created a new site at the same site collection level and security still doesn't work!
One recommendation, NEVER EVER USE INCLUDEUSERSECURITY. I have been burned twice now. IT BREAKS SHAREPOINT.
SharePoint Server 2007
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