By testing the previous instructions for a full crosgrade I run into trouble. Here is the results of my tests to do a full crossgrade of a minimal installation of Debian inside a VM.

First you need to install a 64bits kernel and boot with it. See my previous post on how to do it.

Second you need to do a bootstrap of crossgrading:

 apt-get clean
 apt-get upgrade
 apt-get --download-only install dpkg:amd64 tar:amd64 apt:amd64 bash:amd64 dash:amd64 init:amd64
 dpkg --install /var/cache/apt/archives/*_amd64.deb
 dpkg --install /var/cache/apt/archives/*_amd64.deb
 dpkg --print-architecture
 dpkg --print-foreign-architectures
 apt-get --fix-broken --allow-remove-essential install

Third do a full crossgrade:

 apt-get install --allow-remove-essential $(dpkg --list | grep :i386 | awk '{print $2}' | sed -e s/:i386// )

This procedure seams to be a little fragile, but worked most of the time for me.