I fixed the site bdii problem i.e. the site static information 'disappeared'. It didn't actually disappear it was just declared under mds-vo-name=resource instead of mds-vo-name=UKI-NORTHGRID-MAN-HEP AND THEREFORE GSTAT COULDN'T FIND IT. This was due to rgma and site bdii conflict. The rgma bdii (that didn't exist in very old versions) needs to be declared in the BDII_REGIONS in YAIM. I knew it but forgot completely I already fixed it when I reinstalled the machine few months ago so I spent a delightful afternoon parsing ldif files and ldap output, hacked the ldif, sort of fixed it and then asked for a proper solution. So... here we go I'm writing it down this time so I can google for myself. On the positive side I upgraded now to the latest version both site and top bdiii and the resource bdii on the CEs. So we now have shiny new attributes like Spec2006 &Co.
I also upgraded the CEs trying to fix our random instability problem which afflicts us. However I upgraded online without reinstalling everything and it makes me a bit nervous thinking that some files that needed change might have not been edited because they already exist. So I will completely reinstall the CEs starting with ce01 today.