This version new a manual intervention because the fdholder interface has changed.
I will show you how to do it, make the following on console (log out for your X session).
I use for the demonstration the database used on the ISO, it means default for the boot and Graphics for the user. Obviously, change it for suit your needs.
We will first remake the database for the boot.
First, erase the current database (you can make a copy before if you want)
$ sudo rm -rf /etc/s6/compiled/default
then compile it from the source
$ sudo s6-rc-compile /etc/s6/compiled/default /etc/s6/boot-rc-serv
be sure that the symlink at /etc/s6/compiled/current point to /etc/s6/compiled/default
now, the database for the boot time is ready
For the database user
First, switch to the default database
$ sudo s6opts switch Default
then erase the compiled Graphics database.
$ sudo s6opts remove_db Graphics
then compile and switch to the fresh compiled database
$ sudo s6opts all Graphics graphics
normaly you have now a fresh database and the current database point to Graphics, you can check it by s6opts list.