Never use SharePoint Designer to edit the filesystem pages (for the purpose of making global changes to ghosted sites). Catastrophic failure may (will) occur. Not sure why but it is mentioned in several articles and books. Use any other text/source editor instead (Visual Studio).
After a page (default.master, xxx.aspx) is unghosted using the SharePoint designer, all changes to the respective file sytem files will not propegate into that particular site.
To backup a single site with stsadm when the SharePoint backup/restore process fails, use (
It will create several files.
)...
stsadm -o export -url "http://localhost/site/subsite" -filename "c:\subsite_files\"
To restore...
stsadm -o import -url "http:///site/subsite_b" -filename "c:\subsite_files\site.cmp"
Replace, if necessary, to your domain or machine and port name.