There were two reasons for this:
1) the unprivileged user that runs the BDII is edguser anymore but ldap. Consequently there were some ownership issues in /opt/glite/var subdirectories and files. This was highlighted in /var/log/bdii/bdii-update.log by permission denied errors which I overlooked for a bit too long. Permissions should be as follow: /opt/glite/var /opt/glite/var/lock, /opt/glite/var/tmp and /opt/glite/var/cache should belong to root and anything below them should belong to ldap. You can check if there is anything that doesn't belong to ldap running
find /opt/glite/var/ ! -user ldap -ls
this will include the top directories above which you can ignore.
2) bdii-update doesn't use anymore glite-info-wrapper and glite-info-generic which used to write the .ldif files in the same directory tree above. It now writes what it needs in /var/run/bdii databases and one unique file new.ldif file calling directly the scripts in /opt/glite/etc/gip/provider and /opt/glite/etc/gip/plugin. I upgraded from an older version and the old providers weren't deleted but continued to be executed by bdii-update. Some of them still read what now are obsolete .ldif.
With these two changes, i.e. fixing the ownership of the directories and deleting osolete .ldif files (or the old providers if one is sure of which ones) the site bdii restarted to update correctly the dynamic attributes.
Finally a note on making it easier to reinstall: in the previous post I suggested to add manually SLAPD=/usr/sbin/slapd2.4 to change slapd version to the newly installed /opt/bdii/etc/bdii.conf. However an easier way to maintain the service in case it needs reinstallation is to add SLAPD=/usr/sbin/slapd2.4 to site-info.def so that when YAIM runs it gets added to /etc/sysconfig/bdii and doesn't need a manual step is the machine is reinstalled.